Purpose: Remove Ensembl (ESNG) gene identifier in the mutation frequency tables, including SNV, CNV and fusion, TPM summary statistics and methylation summary tables that are not in Open Targets target list, and updated to match Open Target disease list.

Usage

To run this from the command line, use:

Rscript -e "rmarkdown::render('01-filter-mtp-tables-for-current-gencode.Rmd', clean = TRUE)"

This assumes you are in the modules directory of the repository, OpenPedCan-analysis/analyses/filter-mutation-frequency-tables.

Setup

Load libraries

# R analysis packages
suppressWarnings(
  suppressPackageStartupMessages(library(rtracklayer))
)
suppressPackageStartupMessages(library(tidyverse))
suppressPackageStartupMessages(library(data.table))
suppressPackageStartupMessages(library(jsonlite))

# Magrittr pipe
`%>%` <- dplyr::`%>%`

Set up directories.

# directories for input and output files
root_dir <- rprojroot::find_root(rprojroot::has_dir(".git"))
data_dir <- file.path(root_dir, "data")
scratch_dir <- file.path(root_dir, "scratch")
analyses_dir <- file.path(root_dir, "analyses")
module_dir <- file.path(analyses_dir, "filter-mtp-tables")
mtp_annot_results_dir <- file.path(analyses_dir,  "mtp-annotations/results")
gene_match_input_dir <- file.path(analyses_dir,  "gene_match/input")
input_dir <- file.path(scratch_dir,  "mtp-commit")
output_dir <- file.path(scratch_dir,  "mtp-filtered")
results_dir <- file.path(module_dir, "results")

# Create results folder if it doesn't exist
if (!dir.exists(results_dir)) {
  dir.create(results_dir)
}

Get input data

Get Open Targets GENCODE Ensembl identifiers

# filter for gene rows and get ids
ensg_ids <- readr::read_tsv(file.path(mtp_annot_results_dir, 
                                      "mtp-targets-mapping.tsv.gz")) %>% 
  dplyr::pull(gene_id) %>% 
  unique() 
Parsed with column specification:
cols(
  gene_symbol = col_character(),
  gene_id = col_character(),
  transcript_id = col_character()
)

Get PMTL Ensembl identifiers

# filter for gene rows and get ids
pmtl_ids <- readr::read_tsv(file.path(gene_match_input_dir, "PMTL_v3.1.tsv")) %>% 
  dplyr::filter(Ensembl_ID != "Symbol_Not_Found") %>% 
  dplyr::pull(Ensembl_ID) %>% 
  unique() 
Parsed with column specification:
cols(
  Ensembl_ID = col_character(),
  Approved_Symbol = col_character(),
  FDA_Designation = col_character(),
  FDA_Class = col_character(),
  FDA_Target = col_character(),
  Mapping_Description = col_character()
)

Get OpenPedCan sample IDs (Kids_First_Biospecimen_ID)

sample_ids <- readr::read_tsv(file.path(data_dir, "histologies.tsv"), 
                              guess_max = 10000) %>% 
  dplyr::filter(sample_type == "Tumor") %>% 
  dplyr::select(Kids_First_Biospecimen_ID, cohort)
Parsed with column specification:
cols(
  .default = col_character(),
  age_at_diagnosis_days = col_double(),
  OS_days = col_double(),
  EFS_days = col_double(),
  age_last_update_days = col_double(),
  CNS_region = col_logical(),
  normal_fraction = col_double(),
  tumor_fraction = col_double(),
  tumor_ploidy = col_double(),
  age_at_event_days = col_double(),
  age_at_chemo_start = col_double(),
  age_at_radiation_start = col_double(),
  cell_line_composition = col_logical(),
  cell_line_passage = col_logical(),
  tumor_fraction_RFpurify_ABSOLUTE = col_logical(),
  tumor_fraction_RFpurify_ESTIMATE = col_logical(),
  tumor_fraction_LUMP = col_logical(),
  dkfz_v11_methylation_subclass = col_logical(),
  dkfz_v11_methylation_subclass_score = col_logical(),
  dkfz_v12_methylation_subclass = col_logical(),
  dkfz_v12_methylation_subclass_score = col_logical()
  # ... with 2 more columns
)
See spec(...) for full column specifications.
Warning: 22740 parsing failures.
  row                              col           expected            actual                                                     file
19856 CNS_region                       1/0/T/F/TRUE/FALSE Hemispheric       '/home/rstudio/OpenPedCan-analysis/data/histologies.tsv'
19856 tumor_fraction_RFpurify_ABSOLUTE 1/0/T/F/TRUE/FALSE 0.323379333333333 '/home/rstudio/OpenPedCan-analysis/data/histologies.tsv'
19856 tumor_fraction_RFpurify_ESTIMATE 1/0/T/F/TRUE/FALSE 0.687136805       '/home/rstudio/OpenPedCan-analysis/data/histologies.tsv'
19856 tumor_fraction_LUMP              1/0/T/F/TRUE/FALSE 0.554654468118469 '/home/rstudio/OpenPedCan-analysis/data/histologies.tsv'
19856 dkfz_v11_methylation_subclass    1/0/T/F/TRUE/FALSE LGG_DIG_DIA       '/home/rstudio/OpenPedCan-analysis/data/histologies.tsv'
..... ................................ .................. ................. ........................................................
See problems(...) for more details.

Filter mutation frequencies tables

Function to filter for required Ensembl gene identifiers and write to file

filter_mtp_table <- function(mtp_table, ensg_ids, file_name) {
  if ("Gene_Ensembl_ID" %in% colnames(mtp_table)) { 
    # filter mtp table and write to file
    mtp_table <- mtp_table %>%
      dplyr::filter(Gene_Ensembl_ID %in% ensg_ids) %>%
      dplyr::mutate(EFO = 
                      case_when(Disease == "Chordoma" ~ "MONDO_0008978",
                                Disease == "Meningioma" ~ "MONDO_0016642",
                                Disease == "Perineuroma" ~ "MONDO_0019404",
                                Disease == "Wilms tumor" ~ "MONDO_0006058",
                                TRUE ~ EFO)) %>% 
      dplyr::mutate(MONDO = 
                      case_when(Disease == "Perineuroma" ~ "MONDO_0019404",
                                TRUE ~ MONDO)) %>% 
      readr::write_tsv(file.path(output_dir, file_name))
  } else {
    # filter tsv mtp table
    mtp_table <- mtp_table %>% 
      dplyr::filter(targetFromSourceId %in% ensg_ids) %>%
      dplyr::mutate(diseaseFromSourceMappedId = 
                      case_when(Disease == "Chordoma" ~ "MONDO_0008978",
                                Disease == "Meningioma" ~ "MONDO_0016642",
                                Disease == "Perineuroma" ~ "MONDO_0019404",
                                Disease == "Wilms tumor" ~ "MONDO_0006058", 
                                TRUE ~ diseaseFromSourceMappedId)) %>% 
      dplyr::mutate(MONDO = 
                      case_when(Disease == "Perineuroma" ~ "MONDO_0019404",
                                TRUE ~ MONDO)) %>% 
      readr::write_tsv(file.path(output_dir, file_name))
     if (grepl("methyl", file_name)) {
       rds_file <- paste(unlist(str_split(file_name, "\\."))[1], "rds", sep = ".")
       mtp_table %>% readr::write_rds(file.path(output_dir, rds_file), compress = "gz")
     }
  }
return(mtp_table)
}

Gene level SNV frequencies

# read mtp table
mtp_file <- 
  file.path(input_dir, "gene-level-snv-consensus-annotated-mut-freq.tsv.gz")
gene_level_snv <- 
  data.table::fread(mtp_file, sep = "\t", showProgress = FALSE) %>%
    tibble::as_tibble() 
Registered S3 method overwritten by 'R.oo':
  method        from       
  throw.default R.methodsS3
# filter mtp table 
file_name <- basename(mtp_file)
filter_mtp_table(gene_level_snv, ensg_ids, file_name) 
# Ensembl gene identifiers removed
filtered_ensg <- gene_level_snv %>% 
  dplyr::filter(!targetFromSourceId %in% ensg_ids) %>% 
  dplyr::select(Gene_symbol, targetFromSourceId) %>%
  dplyr::rename(Ensembl_ID = targetFromSourceId) %>% 
  dplyr::distinct()

# read the SNV consensus file
consensus_ensg <- data.table::fread(
  file.path(data_dir, "snv-consensus-plus-hotspots.maf.tsv.gz"), 
  select = c("Tumor_Sample_Barcode", "Gene"), showProgress = FALSE) %>% 
  tibble::as_tibble() %>% 
  dplyr::filter(!is.na(Gene)) %>% 
  dplyr::rename(Kids_First_Biospecimen_ID = Tumor_Sample_Barcode) %>% 
  dplyr::distinct()

# merge sample IDs to filtered ENSG IDs
filtered_ensg <- filtered_ensg %>% 
  dplyr::left_join(consensus_ensg, by=c("Ensembl_ID" = "Gene"))

# merge OpenPedCan cohorts to filtered ENSG IDs
filtered_ensg <- filtered_ensg %>% 
  dplyr::left_join(sample_ids, by= "Kids_First_Biospecimen_ID")

# write to file
readr::write_tsv(filtered_ensg,
  file.path(results_dir, 
            "gene-level-snv-consensus-annotated-mut-freq_dropped_ensg.tsv.gz"))

# Display removed ENSEMBL IDs 
filtered_ensg %>% dplyr::select(Ensembl_ID, cohort) %>% 
  dplyr::distinct() %>%
  tidyr::drop_na() %>%  
  table()
                 cohort
Ensembl_ID        GMKF PBTA TARGET
  100128124          0    1      0
  100128787          1    1      0
  100129098          1    1      0
  100129307          1    1      0
  100129385          0    1      0
  100129528          1    1      1
  100129603          1    1      1
  100130301          1    1      1
  100130520          1    1      0
  100131107          1    1      1
  100131211          1    1      0
  100131378          1    1      1
  100131539          1    1      1
  100132074          0    1      1
  100132202          1    1      0
  100132247          0    1      0
  100133315          1    1      1
  100141515          1    1      1
  100191040          0    1      1
  100286986          1    1      1
  100288798          1    1      0
  100289255          0    1      0
  100302652          1    1      1
  100302692          1    1      0
  100302736          0    1      1
  100310812          0    1      0
  100421372          1    1      1
  100463487          1    1      0
  100499466          1    1      1
  100505385          1    1      1
  100505498          1    1      0
  100505502          1    1      1
  100505570          0    1      0
  100505583          1    1      0
  100505841          1    1      1
  100506144          1    1      1
  100506376          1    1      1
  100506851          1    1      0
  100506874          1    1      0
  100506974          1    1      0
  100507002          1    1      0
  100507246          0    1      1
  100507527          1    1      1
  100507607          1    1      0
  100509620          1    1      0
  100526664          1    1      1
  100526693          0    1      1
  100526694          1    1      1
  100526740          1    1      1
  100526760          0    1      1
  100526761          0    1      1
  100526767          1    1      1
  100526772          0    1      1
  100526773          0    1      1
  100526783          1    1      1
  100526794          1    1      1
  100526835          0    1      1
  100526842          1    1      1
  100527943          0    1      1
  100527949          1    1      1
  100528017          0    1      1
  100528021          1    1      1
  100528030          0    1      1
  100528032          1    1      1
  100529063          0    1      1
  100529097          0    1      1
  100529144          0    1      1
  100529240          1    1      1
  100529241          0    1      1
  100529257          1    1      0
  100529261          0    1      1
  100532726          0    1      1
  100532731          0    1      1
  100532736          1    1      1
  100533105          0    1      1
  100533106          0    1      1
  100533181          0    1      1
  100533952          0    1      0
  100533997          1    1      1
  100534592          0    1      1
  100534599          0    1      1
  10060              1    1      1
  100631383          1    1      1
  100652781          1    1      1
  100861540          1    1      1
  100885850          1    1      1
  100996598          1    1      1
  100996645          1    1      0
  100996648          0    1      1
  100996758          1    1      0
  100996928          1    0      1
  101059906          1    1      0
  101059938          0    1      0
  101060341          1    1      0
  101060588          1    1      0
  101060684          1    1      1
  10130              0    1      1
  10178              1    1      1
  101926886          1    1      0
  101926942          1    1      0
  101927286          0    1      1
  101927375          1    1      0
  101927423          1    1      0
  101927434          1    1      0
  101927450          1    1      0
  101927468          1    1      0
  101927484          1    1      0
  101927655          0    1      1
  101927668          1    1      0
  101927745          1    1      0
  101927798          1    1      0
  101928047          0    1      0
  101928077          1    1      0
  101928114          1    1      0
  101928268          0    1      0
  101928451          1    1      1
  101928471          0    1      0
  101928570          1    1      0
  101928682          1    1      0
  101928701          1    1      0
  101928778          0    1      0
  101928882          1    1      0
  101929073          1    1      0
  101929084          1    1      0
  101929144          1    1      0
  101929221          0    1      0
  101929309          1    1      0
  101929321          1    1      0
  101929355          1    1      0
  101929356          1    1      0
  101929563          1    1      0
  101929578          1    1      1
  101929628          1    1      0
  101929937          0    1      1
  101930420          1    1      0
  101930434          1    1      0
  10245              0    1      1
  10251              1    1      1
  102546299          1    1      0
  102723765          1    1      0
  102723789          1    1      0
  102723838          1    1      1
  102723968          1    1      1
  102723971          1    1      0
  102723994          1    1      0
  102724072          1    1      0
  102724081          1    1      0
  102724159          1    1      0
  102724194          0    1      0
  102724265          1    1      0
  102724289          1    1      0
  102724338          0    1      0
  102724380          1    1      0
  102724474          1    1      0
  102724488          1    1      0
  102724533          1    1      0
  102724642          1    1      1
  102724657          1    1      0
  102724849          1    1      0
  102724861          1    1      0
  102724862          1    1      0
  102724971          1    1      0
  102725191          1    1      0
  102800317          0    1      1
  10284              1    1      1
  10298              1    1      1
  103                0    0      1
  10333              0    1      1
  10336              1    1      1
  10349              1    1      1
  103689918          0    1      0
  1038               0    1      1
  10402              1    1      1
  10439              0    0      1
  104472715          1    1      1
  10529              1    1      1
  105369165          1    1      0
  105369250          1    1      0
  105369333          1    1      0
  105369501          1    1      0
  105369591          1    1      0
  105369617          1    1      0
  105369669          1    1      0
  105369715          1    1      0
  105369793          1    1      0
  105369809          1    1      1
  105369869          0    1      1
  105369917          1    1      1
  105369958          1    1      0
  105370025          1    1      0
  105370057          0    1      0
  105370084          1    1      0
  105370130          0    1      0
  105370175          1    1      0
  105370214          1    1      0
  105370236          1    1      0
  105370289          0    1      0
  105370299          1    1      0
  105370314          1    1      0
  105370343          1    1      0
  105370344          1    1      0
  105370361          1    1      0
  105370397          1    1      0
  105370470          1    1      0
  105370475          1    1      0
  105370476          1    1      0
  105370491          1    1      1
  105370507          1    1      0
  105370593          1    1      0
  105370656          1    1      0
  105370673          1    1      0
  105370698          1    1      0
  105370706          1    1      0
  105370739          1    1      0
  105370980          1    1      1
  105371063          0    1      0
  105371233          1    1      0
  105371235          1    1      0
  105371253          1    1      0
  105371278          1    1      0
  105371419          1    1      1
  105371695          1    1      0
  105371811          1    1      0
  105371948          0    1      0
  105371974          1    1      0
  105372019          1    1      0
  105372043          1    1      0
  105372157          1    1      0
  105372186          1    1      0
  105372204          1    1      0
  105372267          1    1      0
  105372358          1    1      0
  105372362          1    1      0
  105372371          1    1      0
  105372399          1    1      0
  105372528          1    1      0
  105372532          1    1      0
  105372562          1    1      0
  105372620          1    1      0
  105372652          1    1      0
  105372704          0    1      0
  105372893          0    1      0
  105372916          1    1      0
  105372923          1    1      0
  105372952          1    1      0
  105373057          1    1      1
  105373091          1    1      0
  105373163          1    1      0
  105373220          1    1      0
  105373261          1    1      0
  105373273          1    1      0
  105373297          1    1      0
  105373346          1    1      0
  105373444          1    1      0
  105373523          1    1      0
  105373553          1    1      0
  105373598          1    1      0
  105373652          1    1      0
  105373727          1    1      0
  105373782          1    1      0
  105373836          1    1      0
  105373893          1    1      0
  105373896          1    1      0
  105373911          1    1      0
  105373941          1    1      0
  105373989          1    1      0
  105374016          1    1      0
  105374033          1    1      0
  105374056          1    1      0
  105374060          1    1      1
  105374094          0    1      0
  105374103          1    1      0
  105374122          1    1      0
  105374138          1    1      0
  105374160          1    1      0
  105374166          1    1      0
  105374301          1    1      0
  105374391          1    1      0
  105374413          1    1      0
  105374483          1    1      0
  105374492          1    1      0
  105374494          1    1      0
  105374525          1    1      0
  105374528          1    1      0
  105374549          1    1      0
  105374594          1    1      0
  105374627          1    1      0
  105374654          1    1      0
  105374769          1    1      0
  105374831          1    1      0
  105374855          1    1      1
  105374942          1    1      0
  105374956          1    1      0
  105374958          1    1      0
  105374970          0    1      0
  105375021          1    1      1
  105375036          1    1      0
  105375107          0    1      0
  105375116          1    1      0
  105375237          1    1      0
  105375278          1    1      0
  105375282          1    1      0
  105375291          1    1      0
  105375299          1    1      0
  105375322          1    1      0
  105375324          1    1      0
  105375337          1    1      0
  105375630          1    1      0
  105375646          1    1      0
  105375670          1    1      0
  105375724          1    1      1
  105375742          1    1      0
  105375749          1    1      0
  105375795          0    0      1
  105375817          1    1      0
  105375851          1    1      0
  105375906          1    1      0
  105375925          1    1      0
  105375937          1    1      0
  105375993          1    1      0
  105376083          1    1      0
  105376084          1    1      0
  105376123          1    1      0
  105376126          1    1      0
  105376135          0    1      0
  105376140          0    1      0
  105376147          1    1      1
  105376166          1    1      0
  105376191          1    1      0
  105376194          1    1      0
  105376244          1    1      0
  105376335          1    1      0
  105376341          1    1      0
  105376367          1    1      0
  105376400          1    1      0
  105376454          1    1      0
  105376625          0    1      0
  105376636          1    1      0
  105376661          1    1      0
  105376714          1    1      1
  105376735          1    1      0
  105376875          1    1      0
  105376876          1    1      0
  105377253          1    1      0
  105377278          1    1      0
  105377296          1    1      0
  105377308          1    1      1
  105377310          1    1      0
  105377350          1    1      0
  105377436          1    1      0
  105377447          0    1      0
  105377513          1    1      0
  105377579          0    1      0
  105377622          1    1      0
  105377663          1    1      0
  105377684          1    1      0
  105377699          1    1      0
  105377705          1    1      0
  105377732          1    1      0
  105377742          1    1      0
  105377781          1    1      1
  105377793          1    1      0
  105377796          1    1      0
  105377805          1    1      1
  105377841          1    1      0
  105377913          1    1      0
  105377959          1    1      0
  105378013          1    1      0
  105378021          1    1      0
  105378071          1    1      0
  105378102          1    1      0
  105378148          1    1      0
  105378193          1    1      0
  105378239          1    1      0
  105378314          1    1      0
  105378407          1    1      0
  105378415          1    1      0
  105378464          1    1      0
  105378532          1    1      1
  105378612          1    1      0
  105378621          1    1      0
  105378644          1    1      0
  105378712          1    1      0
  105378771          1    1      0
  105378776          1    1      0
  105378789          1    1      0
  105378802          1    1      0
  105378849          1    1      0
  105378947          1    1      0
  105378979          1    1      0
  105379100          1    1      1
  105379198          1    1      0
  105379315          1    1      0
  105379337          1    1      0
  105379752          1    1      0
  10658              1    1      0
  10665              1    1      1
  10677              1    1      1
  107181291          1    1      0
  10723              1    1      1
  10739              1    1      1
  107983958          1    1      1
  107983971          1    1      0
  107983981          1    1      1
  107983989          1    1      0
  107983993          0    1      0
  107984005          1    1      0
  107984014          1    1      0
  107984025          1    1      0
  107984083          1    1      0
  107984124          1    1      1
  107984128          1    1      0
  107984175          1    1      0
  107984186          1    1      0
  107984189          1    1      0
  107984203          1    1      0
  107984207          1    1      0
  107984222          1    1      0
  107984264          1    1      0
  107984330          1    1      0
  107984351          1    1      0
  107984449          1    1      0
  107984512          0    1      0
  107984590          1    1      0
  107984638          1    1      0
  107984654          1    1      0
  107984674          1    1      0
  107984817          1    1      0
  107984832          1    1      0
  107984833          1    1      0
  107984862          1    1      0
  107984876          1    1      0
  107984974          1    1      0
  107985021          1    1      0
  107985022          0    1      0
  107985149          1    1      1
  107985178          1    1      0
  107985208          0    1      0
  107985251          1    1      0
  107985385          1    1      0
  107985508          1    1      0
  107985556          1    1      1
  107985637          1    1      0
  107985652          1    1      0
  107985678          0    1      1
  107985729          1    1      0
  107985773          1    1      1
  107985792          1    1      0
  107985795          0    1      0
  107985805          0    1      0
  107985836          1    1      0
  107985866          1    1      0
  107985876          1    1      0
  107985888          0    1      0
  107985924          1    1      0
  107985962          1    1      0
  107985976          1    1      0
  107986022          1    1      1
  107986217          1    1      1
  107986223          1    1      0
  107986265          1    1      1
  107986306          1    1      0
  107986322          1    1      1
  107986332          1    1      0
  107986388          1    1      0
  107986583          1    1      0
  107986617          1    1      0
  107986619          0    1      0
  107986635          1    1      0
  107986668          0    1      0
  107986744          1    1      0
  107986762          1    1      0
  107986806          1    1      1
  107986815          1    1      0
  107986827          1    1      1
  107986902          1    1      0
  107986913          1    1      0
  107986982          1    1      0
  107987042          1    1      0
  107987044          0    1      0
  107987054          1    1      0
  107987067          1    1      0
  107987125          1    1      0
  107987211          1    1      1
  107987238          0    1      0
  107987243          1    1      0
  107987248          1    1      0
  107987269          0    1      0
  107987285          1    1      0
  10810              1    1      0
  10861              1    1      1
  109729166          1    1      0
  110116772          1    1      1
  110117499          0    1      1
  11045              1    1      1
  110599563          0    1      1
  110599583          0    1      1
  110806280          1    1      1
  110806290          1    1      0
  111089941          1    1      1
  11122              1    1      1
  11148              0    1      1
  11158              0    1      1
  11170              0    1      1
  112267855          1    1      0
  112267879          1    1      0
  112267897          1    1      0
  112267904          1    1      1
  112267968          1    1      0
  112268052          0    1      0
  112268076          1    1      0
  112268092          1    1      0
  112268119          1    1      0
  112268145          1    1      0
  112268168          1    1      0
  112268186          1    1      0
  112268444          1    1      0
  11243              0    1      1
  112577516          1    1      1
  112577592          1    1      0
  112694756          1    1      1
  113130             1    1      1
  11346              1    1      1
  114659             1    1      1
  114769             0    1      1
  114780             1    1      1
  114825             1    1      1
  114827             1    1      1
  114841035          0    1      1
  114991             1    1      1
  115072896          1    1      1
  116039             0    1      1
  116804918          1    1      1
  118142757          1    1      1
  1192               0    1      1
  120146             1    1      1
  120376             0    1      1
  121601             1    1      1
  122651             1    1      1
  1234               1    1      1
  1235               1    1      1
  126204             1    1      1
  127943             1    1      1
  128853             0    1      1
  132001             1    1      0
  133688             0    1      0
  134860             0    1      1
  135138             0    1      1
  136332             1    1      1
  137196             1    1      0
  137682             1    1      1
  138241             1    1      0
  138639             1    1      1
  138652             1    1      1
  138715             0    1      1
  139604             0    1      1
  140686             1    1      0
  140699             1    1      1
  140731             1    1      1
  140862             1    1      0
  141                1    1      1
  1432               1    1      0
  143501             1    1      1
  143502             0    1      1
  1438               1    1      0
  144203             1    1      1
  1448               1    1      1
  144983             1    1      1
  1456               1    1      1
  146227             1    1      1
  146433             1    1      1
  146713             1    1      1
  146923             0    1      0
  147                1    1      0
  147166             1    1      1
  148                1    1      0
  148137             0    1      1
  148231             1    1      1
  148345             0    1      0
  1488               1    1      0
  149013             1    1      1
  149708             0    1      1
  150084             1    1      1
  150681             1    1      1
  150684             1    1      1
  150763             0    1      1
  151194             1    1      1
  151648             0    1      1
  1523               0    1      1
  152404             0    0      1
  152742             1    1      0
  152815             1    1      1
  152940             1    1      0
  153090             1    1      1
  155061             1    1      1
  155184             1    1      0
  157567             1    1      1
  157697             1    1      1
  158046             1    1      0
  158055             1    1      1
  158358             1    1      0
  158435             1    1      0
  158931             0    1      1
  159091             1    1      0
  159371             1    1      0
  1600               1    1      0
  160365             1    1      1
  160492             1    1      0
  160857             1    1      0
  161142             1    1      1
  162966             0    1      1
  162972             1    1      1
  1638               1    1      0
  1646               1    1      1
  165679             1    1      1
  165721             0    1      1
  166929             1    1      1
  168975             0    0      1
  169355             0    0      1
  169834             1    1      1
  169966             1    1      1
  170082             1    1      1
  170961             0    1      1
  1767               0    1      0
  1780               1    1      1
  1800               0    1      1
  1936               1    1      1
  1998               0    1      1
  199990             1    1      1
  200008             0    1      1
  200172             1    1      1
  2009               0    1      1
  200959             1    1      1
  201516             1    1      1
  201625             1    1      1
  2036               1    1      0
  2078               1    1      1
  2104               1    1      0
  2187               1    1      1
  219595             1    1      1
  219958             0    1      1
  2205               1    1      1
  221301             1    1      1
  221357             1    1      1
  221946             1    1      0
  222611             1    1      1
  222967             1    1      0
  2258               1    1      1
  2259               0    1      1
  22797              0    1      1
  22829              1    1      1
  22859              1    1      1
  22871              1    1      1
  22903              0    1      0
  22950              1    1      1
  22987              1    1      0
  22995              1    1      1
  22998              0    1      1
  23026              1    1      0
  23031              1    1      1
  23089              1    1      1
  23143              1    1      1
  23199              1    1      1
  23243              0    1      1
  23247              1    1      1
  23254              0    1      1
  23263              0    1      1
  23271              1    1      1
  23353              0    1      1
  23362              0    1      1
  23426              0    0      1
  23499              1    1      1
  23520              1    1      1
  23539              0    0      1
  23543              1    1      1
  23567              0    1      0
  23761              0    1      1
  245913             0    1      1
  246175             1    1      1
  2491               1    1      1
  25                 1    1      1
  2542               0    1      1
  254272             1    1      0
  254773             1    1      1
  2549               0    1      1
  256076             1    1      1
  257313             1    1      1
  25769              1    1      1
  25776              1    1      1
  25777              1    1      1
  25822              1    1      1
  25941              0    1      1
  25945              1    1      1
  25979              1    1      1
  26013              1    1      1
  260293             1    1      1
  26083              1    1      1
  26147              0    1      0
  26231              1    1      1
  26272              1    1      0
  26468              1    1      0
  26609              1    1      1
  267012             0    1      1
  27077              1    1      1
  27094              1    1      1
  27097              1    1      1
  27098              0    1      1
  27141              1    1      1
  27180              1    1      0
  28                 1    1      1
  280664             0    0      1
  28231              1    1      0
  2825               1    1      1
  282966             0    1      1
  282973             1    1      1
  282974             1    1      1
  283463             1    1      1
  283694             0    0      1
  283848             1    1      1
  283982             1    1      1
  284361             1    1      0
  284371             0    1      1
  284498             1    1      1
  284521             1    1      1
  285346             1    1      1
  285362             1    1      1
  285498             1    1      1
  285555             1    1      1
  285834             1    1      0
  2859               1    1      1
  286                0    1      1
  286187             0    1      1
  286223             1    1      1
  286749             1    1      1
  287                1    1      1
  2873               1    1      1
  29058              1    1      1
  2914               0    1      1
  29850              0    1      1
  29914              1    1      1
  29990              1    1      1
  29998              1    1      1
  3012               0    1      1
  3017               0    1      1
  30820              0    1      1
  3084               1    1      1
  3164               1    1      1
  3172               1    1      1
  317703             1    1      0
  3187               1    1      0
  324                1    0      1
  3320               0    1      1
  3338               0    1      1
  338872             1    1      1
  338879             1    1      1
  339501             0    1      0
  339512             1    1      1
  339766             1    1      1
  340069             0    1      1
  340094             0    1      1
  340205             0    1      1
  340441             1    1      1
  340526             1    1      1
  340595             1    1      1
  341346             1    1      1
  342931             1    1      1
  343068             1    1      1
  3441               0    1      1
  344892             1    1      1
  345062             0    1      1
  347169             1    1      1
  347475             1    1      1
  348751             1    1      1
  353149             0    1      1
  3556               1    1      1
  3581               0    1      0
  359710             0    1      1
  359845             1    1      1
  360226             0    1      1
  3609               0    1      1
  3655               0    1      1
  3699               0    1      1
  3712               0    1      1
  373856             1    1      1
  3742               1    1      1
  374286             0    1      0
  374308             1    1      1
  374462             1    1      1
  374864             1    1      1
  374900             0    1      1
  374907             0    1      1
  374986             1    1      1
  375449             1    1      1
  375616             0    1      0
  375748             1    1      1
  375757             0    1      1
  3778               1    1      1
  3801               0    0      1
  3805               0    1      1
  3809               1    1      1
  3811               1    1      1
  3831               0    1      1
  387104             1    1      1
  387263             1    1      1
  387522             1    1      1
  387723             1    1      0
  388199             1    1      1
  388276             0    1      1
  388324             1    1      1
  388677             1    1      1
  388685             1    1      0
  388761             1    1      1
  388795             1    1      1
  388960             0    1      1
  389197             1    1      1
  389199             0    1      1
  389690             1    1      1
  389895             1    1      0
  390226             1    1      1
  390748             1    1      1
  390877             0    1      1
  391003             1    1      1
  392490             1    1      1
  392617             1    1      1
  3983               1    1      1
  400073             1    1      1
  400087             1    1      0
  400499             1    1      1
  400533             1    1      0
  400620             1    1      0
  400797             1    1      0
  400818             1    1      1
  400986             1    1      1
  401067             1    1      1
  401082             1    1      1
  401115             1    1      1
  401149             1    1      0
  401237             1    1      1
  401399             1    1      1
  401497             0    1      0
  401992             1    1      1
  401994             1    1      1
  402160             1    1      1
  4033               0    1      0
  403323             1    1      0
  403341             1    1      1
  404734             1    1      1
  407977             0    1      1
  408186             1    1      1
  414061             0    1      1
  4168               1    1      1
  4174               1    1      0
  433                0    1      1
  439915             0    1      1
  440348             1    1      1
  440352             1    1      1
  440353             1    1      1
  440556             1    1      1
  440689             1    1      1
  440896             1    1      0
  440993             1    1      1
  441108             0    0      1
  441155             1    1      1
  441239             0    1      0
  441251             1    1      1
  441452             1    1      1
  441459             1    1      1
  441525             1    1      1
  441631             1    1      0
  441669             1    1      0
  441911             1    1      1
  442179             1    1      0
  445347             1    1      1
  445372             0    1      1
  445815             1    1      1
  448834             1    1      1
  4583               1    1      1
  463                1    1      1
  4636               1    1      1
  474354             1    1      1
  4802               0    1      1
  4883               0    0      1
  493754             1    1      0
  493901             0    1      1
  4946               0    1      1
  4948               1    1      0
  4957               1    1      1
  4988               0    1      1
  4992               1    1      1
  4995               1    1      1
  503834             1    1      1
  50514              1    1      1
  50636              0    1      1
  50650              0    1      1
  5099               1    1      1
  51031              1    1      1
  51043              1    1      1
  51088              1    1      0
  51207              0    1      1
  51265              1    1      0
  51266              1    1      1
  51351              1    1      1
  5136               1    1      1
  5137               1    1      1
  5143               1    1      1
  51435              1    1      0
  5144               0    1      1
  51466              1    1      0
  5154               0    1      0
  51557              1    1      0
  51686              1    1      1
  5217               0    1      1
  5271               1    1      0
  5308               0    1      1
  5320               0    1      1
  53354              1    1      1
  5339               0    1      1
  53405              1    1      1
  53616              0    0      1
  53632              1    1      1
  54097              1    1      1
  5430               1    1      1
  54331              1    1      1
  54332              0    1      0
  5437               0    1      1
  54536              0    0      1
  54585              0    0      1
  5475               1    1      1
  54825              1    1      1
  548644             1    1      1
  54914              1    1      1
  5495               1    1      1
  54970              0    1      0
  54998              0    1      1
  55                 1    1      1
  55041              1    1      1
  55179              0    1      1
  5522               0    1      1
  55267              1    1      1
  5527               1    1      1
  55284              0    1      1
  552891             0    1      1
  55297              0    1      1
  553158             0    1      1
  55324              1    1      1
  55350              0    1      1
  55384              1    1      1
  55507              1    1      1
  55521              0    1      1
  55567              1    1      1
  55672              1    1      1
  55715              0    1      1
  55734              0    1      1
  55769              1    1      1
  55793              1    1      1
  55809              1    1      1
  55819              1    1      1
  55841              1    1      1
  55959              1    1      1
  55964              1    1      1
  56165              1    1      1
  56341              0    1      1
  5646               0    1      1
  56606              1    1      0
  56658              0    1      1
  56901              0    1      1
  56907              1    1      1
  56911              1    1      1
  56918              1    1      1
  56924              0    1      1
  56938              1    1      1
  56955              1    1      1
  5697               1    1      1
  56971              1    1      1
  56977              0    1      0
  57002              0    1      1
  57047              1    1      1
  57093              1    1      0
  57153              1    1      1
  57180              1    1      0
  5733               1    1      1
  57451              1    1      1
  57480              1    1      1
  57489              1    1      1
  57529              1    1      1
  57571              1    1      1
  57583              1    1      1
  57624              1    1      1
  57642              1    1      1
  57644              0    0      1
  57674              0    1      1
  57690              1    1      1
  57705              1    1      1
  57821              1    1      1
  57835              1    1      1
  5900               0    0      1
  5906               1    1      1
  5983               1    1      1
  5988               1    1      1
  5998               1    1      1
  6006               1    1      1
  60312              1    1      1
  60437              1    1      1
  60487              1    1      0
  60490              1    1      0
  60506              1    1      1
  6092               1    1      1
  6101               1    1      1
  613037             0    1      0
  613211             1    1      1
  613227             1    1      1
  6196               0    1      1
  6276               0    1      1
  631                1    1      1
  6370               0    1      1
  64067              1    1      1
  64097              1    1      1
  641517             1    1      1
  642484             1    1      1
  642515             0    1      1
  642612             1    1      1
  642799             0    1      0
  642819             1    1      1
  643311             0    1      1
  643314             0    1      1
  643376             1    1      1
  643382             1    1      1
  64342              1    1      0
  643723             1    1      0
  644100             1    1      1
  645191             1    1      1
  645202             1    1      1
  645369             1    1      1
  645414             1    1      1
  645425             1    1      1
  64582              1    1      1
  646262             1    1      1
  646588             1    1      0
  646915             1    1      0
  647264             1    1      0
  64756              0    1      1
  64770              1    1      1
  64860              0    1      1
  650226             1    1      0
  65109              0    1      0
  65249              0    1      0
  65265              0    1      0
  653061             1    1      1
  653149             1    1      1
  653857             1    1      0
  654231             1    1      1
  65982              0    0      1
  65983              0    1      1
  6675               0    1      1
  6698               1    1      1
  6733               1    1      0
  6757               0    0      1
  6788               1    1      1
  6867               0    1      1
  692312             0    1      1
  7005               1    1      1
  7037               1    1      1
  7082               0    1      1
  7089               0    1      1
  7182               0    1      1
  7275               1    1      1
  727800             0    1      1
  728194             1    1      0
  728392             1    1      1
  728441             1    1      1
  728588             1    1      1
  728763             1    1      1
  728888             1    1      1
  728957             1    1      1
  728989             1    1      1
  729218             1    1      0
  729262             0    1      0
  729359             1    1      1
  729428             1    1      1
  729767             0    1      1
  729978             1    1      1
  730005             0    0      1
  730098             1    1      1
  731275             1    1      1
  7402               1    1      1
  7417               0    1      1
  7422               1    0      1
  744                1    1      1
  7466               1    1      0
  7494               0    1      1
  7547               0    0      1
  7587               0    1      1
  7594               0    1      0
  7644               1    1      0
  767558             0    0      1
  7739               1    1      1
  7757               0    1      0
  7767               1    1      1
  777                0    1      0
  7771               0    1      1
  7775               1    1      1
  7798               1    1      1
  79015              1    1      0
  79020              1    1      1
  79037              0    1      1
  79081              0    1      1
  79091              1    1      0
  79470              1    1      1
  79589              0    1      1
  79676              1    1      1
  79750              1    1      0
  79784              0    1      0
  79917              0    1      1
  79921              0    1      1
  79931              0    1      1
  79949              0    1      1
  80036              0    0      1
  80095              1    1      1
  80125              1    1      1
  80254              0    1      1
  80728              1    1      1
  80741              0    1      1
  80817              1    1      1
  80833              1    1      1
  80854              0    1      1
  81328              1    1      1
  81458              1    1      1
  81889              0    1      1
  8225               0    1      1
  83259              1    1      1
  83463              0    1      1
  8347               1    1      1
  83551              0    1      1
  84253              0    0      1
  84309              1    1      1
  84337              0    1      1
  84460              0    1      1
  8453               0    1      0
  84614              1    1      1
  8470               1    1      1
  84725              0    1      1
  84750              1    1      0
  84765              1    1      1
  84790              0    1      1
  84808              1    1      1
  84851              1    1      1
  84876              0    1      1
  84924              1    1      1
  84985              1    1      1
  8525               1    1      1
  85358              1    1      1
  85395              0    1      1
  85397              1    1      1
  85439              1    1      1
  85441              1    1      1
  85452              1    1      1
  8638               0    1      0
  8668               0    1      1
  8681               1    1      1
  8711               0    1      1
  8785               1    1      1
  8801               0    1      1
  8857               1    1      1
  89780              1    1      0
  89795              0    1      1
  89796              1    1      1
  8996               0    1      1
  90007              1    1      1
  90019              1    1      1
  90050              1    1      1
  90113              1    1      1
  90293              1    1      1
  9033               1    1      0
  90362              1    1      1
  9038               1    1      1
  90416              1    1      1
  90417              0    1      1
  90523              1    1      0
  90850              1    1      1
  91227              0    1      0
  91526              0    1      0
  9154               1    1      1
  91544              1    1      1
  91646              1    1      1
  91833              1    1      1
  91869              1    1      0
  92292              1    1      1
  9274               0    1      1
  92806              1    1      1
  92949              0    1      0
  93594              1    1      0
  94025              1    1      0
  94121              1    1      1
  9425               0    1      1
  9478               1    1      1
  9498               0    1      1
  9534               1    1      0
  9612               1    1      1
  9628               1    1      0
  9645               1    1      1
  9651               1    1      1
  9686               1    1      1
  9693               1    1      1
  9721               1    1      1
  9734               1    1      1
  9738               1    1      1
  9745               1    1      0
  9758               0    1      0
  9887               1    1      1
  9906               1    1      1
  9922               0    1      0
  9942               1    1      0
  9994               1    1      1
  ENSG00000112096    1    1      1
  ENSG00000182230    1    1      1
  ENSG00000215271    1    1      1
  ENSG00000221995    1    1      1
  ENSG00000249860    1    1      1
  ENSG00000256045    1    1      1
  ENSG00000256222    1    1      1
  ENSG00000256892    1    1      0
  ENSG00000269028    1    1      0
  ENSG00000270188    1    1      0
  ENSG00000270394    1    1      0
# Display samples in removed ENSEMBL IDs that are in PMTL list
filtered_ensg %>% dplyr::filter(Ensembl_ID %in% pmtl_ids) %>% 
  select(Ensembl_ID, Kids_First_Biospecimen_ID) %>% 
  dplyr::distinct()
# Remove data frames
rm(gene_level_snv, filtered_ensg)

Variant level SNV frequencies

# read mtp table
mtp_file <- 
  file.path(input_dir, "variant-level-snv-consensus-annotated-mut-freq.tsv.gz")
variant_level_snv <- 
  data.table::fread(mtp_file, sep = "\t", showProgress = FALSE) %>%
    tibble::as_tibble() 
# filter mtp table
file_name <- basename(mtp_file)
filter_mtp_table(variant_level_snv, ensg_ids, file_name) 
# Ensembl gene identifiers removed
filtered_ensg <- variant_level_snv %>% 
  dplyr::filter(!targetFromSourceId %in% ensg_ids) %>% 
  dplyr::select(Gene_symbol, targetFromSourceId) %>%
  dplyr::rename(Ensembl_ID = targetFromSourceId) %>% 
  dplyr::distinct()

# merge sample IDs to filtered ENSG IDs
filtered_ensg <- filtered_ensg %>% 
  dplyr::left_join(consensus_ensg, by=c("Ensembl_ID" = "Gene"))

# merge OpenPedCan cohorts to filtered ENSG IDs
filtered_ensg <- filtered_ensg %>% 
  dplyr::left_join(sample_ids, by= "Kids_First_Biospecimen_ID")

# write to file
readr::write_tsv(filtered_ensg,
  file.path(results_dir, 
            "variant-level-snv-consensus-annotated-mut-freq_dropped_ensg.tsv.gz"))

# Display removed ENSEMBL IDs 
filtered_ensg %>% dplyr::select(Ensembl_ID, cohort) %>% 
  dplyr::distinct() %>%
  tidyr::drop_na() %>% 
  table()
                 cohort
Ensembl_ID        GMKF PBTA TARGET
  100128124          0    1      0
  100128787          1    1      0
  100129098          1    1      0
  100129307          1    1      0
  100129385          0    1      0
  100129528          1    1      1
  100129603          1    1      1
  100130301          1    1      1
  100130520          1    1      0
  100131107          1    1      1
  100131211          1    1      0
  100131378          1    1      1
  100131539          1    1      1
  100132074          0    1      1
  100132202          1    1      0
  100132247          0    1      0
  100133315          1    1      1
  100141515          1    1      1
  100191040          0    1      1
  100286986          1    1      1
  100288798          1    1      0
  100289255          0    1      0
  100302652          1    1      1
  100302692          1    1      0
  100302736          0    1      1
  100310812          0    1      0
  100421372          1    1      1
  100463487          1    1      0
  100499466          1    1      1
  100505385          1    1      1
  100505498          1    1      0
  100505502          1    1      1
  100505570          0    1      0
  100505583          1    1      0
  100505841          1    1      1
  100506144          1    1      1
  100506376          1    1      1
  100506851          1    1      0
  100506874          1    1      0
  100506974          1    1      0
  100507002          1    1      0
  100507246          0    1      1
  100507527          1    1      1
  100507607          1    1      0
  100509620          1    1      0
  100526664          1    1      1
  100526693          0    1      1
  100526694          1    1      1
  100526740          1    1      1
  100526760          0    1      1
  100526761          0    1      1
  100526767          1    1      1
  100526772          0    1      1
  100526773          0    1      1
  100526783          1    1      1
  100526794          1    1      1
  100526835          0    1      1
  100526842          1    1      1
  100527943          0    1      1
  100527949          1    1      1
  100528017          0    1      1
  100528021          1    1      1
  100528030          0    1      1
  100528032          1    1      1
  100529063          0    1      1
  100529097          0    1      1
  100529144          0    1      1
  100529240          1    1      1
  100529241          0    1      1
  100529257          1    1      0
  100529261          0    1      1
  100532726          0    1      1
  100532731          0    1      1
  100532736          1    1      1
  100533105          0    1      1
  100533106          0    1      1
  100533181          0    1      1
  100533952          0    1      0
  100533997          1    1      1
  100534592          0    1      1
  100534599          0    1      1
  10060              1    1      1
  100631383          1    1      1
  100652781          1    1      1
  100861540          1    1      1
  100885850          1    1      1
  100996598          1    1      1
  100996645          1    1      0
  100996648          0    1      1
  100996758          1    1      0
  100996928          1    0      1
  101059906          1    1      0
  101059938          0    1      0
  101060341          1    1      0
  101060588          1    1      0
  101060684          1    1      1
  10130              0    1      1
  10178              1    1      1
  101926886          1    1      0
  101926942          1    1      0
  101927286          0    1      1
  101927375          1    1      0
  101927423          1    1      0
  101927434          1    1      0
  101927450          1    1      0
  101927468          1    1      0
  101927484          1    1      0
  101927655          0    1      1
  101927668          1    1      0
  101927745          1    1      0
  101927798          1    1      0
  101928047          0    1      0
  101928077          1    1      0
  101928114          1    1      0
  101928268          0    1      0
  101928451          1    1      1
  101928471          0    1      0
  101928570          1    1      0
  101928682          1    1      0
  101928701          1    1      0
  101928778          0    1      0
  101928882          1    1      0
  101929073          1    1      0
  101929084          1    1      0
  101929144          1    1      0
  101929221          0    1      0
  101929309          1    1      0
  101929321          1    1      0
  101929355          1    1      0
  101929356          1    1      0
  101929563          1    1      0
  101929578          1    1      1
  101929628          1    1      0
  101929937          0    1      1
  101930420          1    1      0
  101930434          1    1      0
  10245              0    1      1
  10251              1    1      1
  102546299          1    1      0
  102723765          1    1      0
  102723789          1    1      0
  102723838          1    1      1
  102723968          1    1      1
  102723971          1    1      0
  102723994          1    1      0
  102724072          1    1      0
  102724081          1    1      0
  102724159          1    1      0
  102724194          0    1      0
  102724265          1    1      0
  102724289          1    1      0
  102724338          0    1      0
  102724380          1    1      0
  102724474          1    1      0
  102724488          1    1      0
  102724533          1    1      0
  102724642          1    1      1
  102724657          1    1      0
  102724849          1    1      0
  102724861          1    1      0
  102724862          1    1      0
  102724971          1    1      0
  102725191          1    1      0
  102800317          0    1      1
  10284              1    1      1
  10298              1    1      1
  103                0    0      1
  10333              0    1      1
  10336              1    1      1
  10349              1    1      1
  103689918          0    1      0
  1038               0    1      1
  10402              1    1      1
  10439              0    0      1
  104472715          1    1      1
  10529              1    1      1
  105369165          1    1      0
  105369250          1    1      0
  105369333          1    1      0
  105369501          1    1      0
  105369591          1    1      0
  105369617          1    1      0
  105369669          1    1      0
  105369715          1    1      0
  105369793          1    1      0
  105369809          1    1      1
  105369869          0    1      1
  105369917          1    1      1
  105369958          1    1      0
  105370025          1    1      0
  105370057          0    1      0
  105370084          1    1      0
  105370130          0    1      0
  105370175          1    1      0
  105370214          1    1      0
  105370236          1    1      0
  105370289          0    1      0
  105370299          1    1      0
  105370314          1    1      0
  105370343          1    1      0
  105370344          1    1      0
  105370361          1    1      0
  105370397          1    1      0
  105370470          1    1      0
  105370475          1    1      0
  105370476          1    1      0
  105370491          1    1      1
  105370507          1    1      0
  105370593          1    1      0
  105370656          1    1      0
  105370673          1    1      0
  105370698          1    1      0
  105370706          1    1      0
  105370739          1    1      0
  105370980          1    1      1
  105371063          0    1      0
  105371233          1    1      0
  105371235          1    1      0
  105371253          1    1      0
  105371278          1    1      0
  105371419          1    1      1
  105371695          1    1      0
  105371811          1    1      0
  105371948          0    1      0
  105371974          1    1      0
  105372019          1    1      0
  105372043          1    1      0
  105372157          1    1      0
  105372186          1    1      0
  105372204          1    1      0
  105372267          1    1      0
  105372358          1    1      0
  105372362          1    1      0
  105372371          1    1      0
  105372399          1    1      0
  105372528          1    1      0
  105372532          1    1      0
  105372562          1    1      0
  105372620          1    1      0
  105372652          1    1      0
  105372704          0    1      0
  105372893          0    1      0
  105372916          1    1      0
  105372923          1    1      0
  105372952          1    1      0
  105373057          1    1      1
  105373091          1    1      0
  105373163          1    1      0
  105373220          1    1      0
  105373261          1    1      0
  105373273          1    1      0
  105373297          1    1      0
  105373346          1    1      0
  105373444          1    1      0
  105373523          1    1      0
  105373553          1    1      0
  105373598          1    1      0
  105373652          1    1      0
  105373727          1    1      0
  105373782          1    1      0
  105373836          1    1      0
  105373893          1    1      0
  105373896          1    1      0
  105373911          1    1      0
  105373941          1    1      0
  105373989          1    1      0
  105374016          1    1      0
  105374033          1    1      0
  105374056          1    1      0
  105374060          1    1      1
  105374094          0    1      0
  105374103          1    1      0
  105374122          1    1      0
  105374138          1    1      0
  105374160          1    1      0
  105374166          1    1      0
  105374301          1    1      0
  105374391          1    1      0
  105374413          1    1      0
  105374483          1    1      0
  105374492          1    1      0
  105374494          1    1      0
  105374525          1    1      0
  105374528          1    1      0
  105374549          1    1      0
  105374594          1    1      0
  105374627          1    1      0
  105374654          1    1      0
  105374769          1    1      0
  105374831          1    1      0
  105374855          1    1      1
  105374942          1    1      0
  105374956          1    1      0
  105374958          1    1      0
  105374970          0    1      0
  105375021          1    1      1
  105375036          1    1      0
  105375107          0    1      0
  105375116          1    1      0
  105375237          1    1      0
  105375278          1    1      0
  105375282          1    1      0
  105375291          1    1      0
  105375299          1    1      0
  105375322          1    1      0
  105375324          1    1      0
  105375337          1    1      0
  105375630          1    1      0
  105375646          1    1      0
  105375670          1    1      0
  105375724          1    1      1
  105375742          1    1      0
  105375749          1    1      0
  105375795          0    0      1
  105375817          1    1      0
  105375851          1    1      0
  105375906          1    1      0
  105375925          1    1      0
  105375937          1    1      0
  105375993          1    1      0
  105376083          1    1      0
  105376084          1    1      0
  105376123          1    1      0
  105376126          1    1      0
  105376135          0    1      0
  105376140          0    1      0
  105376147          1    1      1
  105376166          1    1      0
  105376191          1    1      0
  105376194          1    1      0
  105376244          1    1      0
  105376335          1    1      0
  105376341          1    1      0
  105376367          1    1      0
  105376400          1    1      0
  105376454          1    1      0
  105376625          0    1      0
  105376636          1    1      0
  105376661          1    1      0
  105376714          1    1      1
  105376735          1    1      0
  105376875          1    1      0
  105376876          1    1      0
  105377253          1    1      0
  105377278          1    1      0
  105377296          1    1      0
  105377308          1    1      1
  105377310          1    1      0
  105377350          1    1      0
  105377436          1    1      0
  105377447          0    1      0
  105377513          1    1      0
  105377579          0    1      0
  105377622          1    1      0
  105377663          1    1      0
  105377684          1    1      0
  105377699          1    1      0
  105377705          1    1      0
  105377732          1    1      0
  105377742          1    1      0
  105377781          1    1      1
  105377793          1    1      0
  105377796          1    1      0
  105377805          1    1      1
  105377841          1    1      0
  105377913          1    1      0
  105377959          1    1      0
  105378013          1    1      0
  105378021          1    1      0
  105378071          1    1      0
  105378102          1    1      0
  105378148          1    1      0
  105378193          1    1      0
  105378239          1    1      0
  105378314          1    1      0
  105378407          1    1      0
  105378415          1    1      0
  105378464          1    1      0
  105378532          1    1      1
  105378612          1    1      0
  105378621          1    1      0
  105378644          1    1      0
  105378712          1    1      0
  105378771          1    1      0
  105378776          1    1      0
  105378789          1    1      0
  105378802          1    1      0
  105378849          1    1      0
  105378947          1    1      0
  105378979          1    1      0
  105379100          1    1      1
  105379198          1    1      0
  105379315          1    1      0
  105379337          1    1      0
  105379752          1    1      0
  10658              1    1      0
  10665              1    1      1
  10677              1    1      1
  107181291          1    1      0
  10723              1    1      1
  10739              1    1      1
  107983958          1    1      1
  107983971          1    1      0
  107983981          1    1      1
  107983989          1    1      0
  107983993          0    1      0
  107984005          1    1      0
  107984014          1    1      0
  107984025          1    1      0
  107984083          1    1      0
  107984124          1    1      1
  107984128          1    1      0
  107984175          1    1      0
  107984186          1    1      0
  107984189          1    1      0
  107984203          1    1      0
  107984207          1    1      0
  107984222          1    1      0
  107984264          1    1      0
  107984330          1    1      0
  107984351          1    1      0
  107984449          1    1      0
  107984512          0    1      0
  107984590          1    1      0
  107984638          1    1      0
  107984654          1    1      0
  107984674          1    1      0
  107984817          1    1      0
  107984832          1    1      0
  107984833          1    1      0
  107984862          1    1      0
  107984876          1    1      0
  107984974          1    1      0
  107985021          1    1      0
  107985022          0    1      0
  107985149          1    1      1
  107985178          1    1      0
  107985208          0    1      0
  107985251          1    1      0
  107985385          1    1      0
  107985508          1    1      0
  107985556          1    1      1
  107985637          1    1      0
  107985652          1    1      0
  107985678          0    1      1
  107985729          1    1      0
  107985773          1    1      1
  107985792          1    1      0
  107985795          0    1      0
  107985805          0    1      0
  107985836          1    1      0
  107985866          1    1      0
  107985876          1    1      0
  107985888          0    1      0
  107985924          1    1      0
  107985962          1    1      0
  107985976          1    1      0
  107986022          1    1      1
  107986217          1    1      1
  107986223          1    1      0
  107986265          1    1      1
  107986306          1    1      0
  107986322          1    1      1
  107986332          1    1      0
  107986388          1    1      0
  107986583          1    1      0
  107986617          1    1      0
  107986619          0    1      0
  107986635          1    1      0
  107986668          0    1      0
  107986744          1    1      0
  107986762          1    1      0
  107986806          1    1      1
  107986815          1    1      0
  107986827          1    1      1
  107986902          1    1      0
  107986913          1    1      0
  107986982          1    1      0
  107987042          1    1      0
  107987044          0    1      0
  107987054          1    1      0
  107987067          1    1      0
  107987125          1    1      0
  107987211          1    1      1
  107987238          0    1      0
  107987243          1    1      0
  107987248          1    1      0
  107987269          0    1      0
  107987285          1    1      0
  10810              1    1      0
  10861              1    1      1
  109729166          1    1      0
  110116772          1    1      1
  110117499          0    1      1
  11045              1    1      1
  110599563          0    1      1
  110599583          0    1      1
  110806280          1    1      1
  110806290          1    1      0
  111089941          1    1      1
  11122              1    1      1
  11148              0    1      1
  11158              0    1      1
  11170              0    1      1
  112267855          1    1      0
  112267879          1    1      0
  112267897          1    1      0
  112267904          1    1      1
  112267968          1    1      0
  112268052          0    1      0
  112268076          1    1      0
  112268092          1    1      0
  112268119          1    1      0
  112268145          1    1      0
  112268168          1    1      0
  112268186          1    1      0
  112268444          1    1      0
  11243              0    1      1
  112577516          1    1      1
  112577592          1    1      0
  112694756          1    1      1
  113130             1    1      1
  11346              1    1      1
  114659             1    1      1
  114769             0    1      1
  114780             1    1      1
  114825             1    1      1
  114827             1    1      1
  114841035          0    1      1
  114991             1    1      1
  115072896          1    1      1
  116039             0    1      1
  116804918          1    1      1
  118142757          1    1      1
  1192               0    1      1
  120146             1    1      1
  120376             0    1      1
  121601             1    1      1
  122651             1    1      1
  1234               1    1      1
  1235               1    1      1
  126204             1    1      1
  127943             1    1      1
  128853             0    1      1
  132001             1    1      0
  133688             0    1      0
  134860             0    1      1
  135138             0    1      1
  136332             1    1      1
  137196             1    1      0
  137682             1    1      1
  138241             1    1      0
  138639             1    1      1
  138652             1    1      1
  138715             0    1      1
  139604             0    1      1
  140686             1    1      0
  140699             1    1      1
  140731             1    1      1
  140862             1    1      0
  141                1    1      1
  1432               1    1      0
  143501             1    1      1
  143502             0    1      1
  1438               1    1      0
  144203             1    1      1
  1448               1    1      1
  144983             1    1      1
  1456               1    1      1
  146227             1    1      1
  146433             1    1      1
  146713             1    1      1
  146923             0    1      0
  147                1    1      0
  147166             1    1      1
  148                1    1      0
  148137             0    1      1
  148231             1    1      1
  148345             0    1      0
  1488               1    1      0
  149013             1    1      1
  149708             0    1      1
  150084             1    1      1
  150681             1    1      1
  150684             1    1      1
  150763             0    1      1
  151194             1    1      1
  151648             0    1      1
  1523               0    1      1
  152404             0    0      1
  152742             1    1      0
  152815             1    1      1
  152940             1    1      0
  153090             1    1      1
  155061             1    1      1
  155184             1    1      0
  157567             1    1      1
  157697             1    1      1
  158046             1    1      0
  158055             1    1      1
  158358             1    1      0
  158435             1    1      0
  158931             0    1      1
  159091             1    1      0
  159371             1    1      0
  1600               1    1      0
  160365             1    1      1
  160492             1    1      0
  160857             1    1      0
  161142             1    1      1
  162966             0    1      1
  162972             1    1      1
  1638               1    1      0
  1646               1    1      1
  165679             1    1      1
  165721             0    1      1
  166929             1    1      1
  168975             0    0      1
  169355             0    0      1
  169834             1    1      1
  169966             1    1      1
  170082             1    1      1
  170961             0    1      1
  1767               0    1      0
  1780               1    1      1
  1800               0    1      1
  1936               1    1      1
  1998               0    1      1
  199990             1    1      1
  200008             0    1      1
  200172             1    1      1
  2009               0    1      1
  200959             1    1      1
  201516             1    1      1
  201625             1    1      1
  2036               1    1      0
  2078               1    1      1
  2104               1    1      0
  2187               1    1      1
  219595             1    1      1
  219958             0    1      1
  2205               1    1      1
  221301             1    1      1
  221357             1    1      1
  221946             1    1      0
  222611             1    1      1
  222967             1    1      0
  2258               1    1      1
  2259               0    1      1
  22797              0    1      1
  22829              1    1      1
  22859              1    1      1
  22871              1    1      1
  22903              0    1      0
  22950              1    1      1
  22987              1    1      0
  22995              1    1      1
  22998              0    1      1
  23026              1    1      0
  23031              1    1      1
  23089              1    1      1
  23143              1    1      1
  23199              1    1      1
  23243              0    1      1
  23247              1    1      1
  23254              0    1      1
  23263              0    1      1
  23271              1    1      1
  23353              0    1      1
  23362              0    1      1
  23426              0    0      1
  23499              1    1      1
  23520              1    1      1
  23539              0    0      1
  23543              1    1      1
  23567              0    1      0
  23761              0    1      1
  245913             0    1      1
  246175             1    1      1
  2491               1    1      1
  25                 1    1      1
  2542               0    1      1
  254272             1    1      0
  254773             1    1      1
  2549               0    1      1
  256076             1    1      1
  257313             1    1      1
  25769              1    1      1
  25776              1    1      1
  25777              1    1      1
  25822              1    1      1
  25941              0    1      1
  25945              1    1      1
  25979              1    1      1
  26013              1    1      1
  260293             1    1      1
  26083              1    1      1
  26147              0    1      0
  26231              1    1      1
  26272              1    1      0
  26468              1    1      0
  26609              1    1      1
  267012             0    1      1
  27077              1    1      1
  27094              1    1      1
  27097              1    1      1
  27098              0    1      1
  27141              1    1      1
  27180              1    1      0
  28                 1    1      1
  280664             0    0      1
  28231              1    1      0
  2825               1    1      1
  282966             0    1      1
  282973             1    1      1
  282974             1    1      1
  283463             1    1      1
  283694             0    0      1
  283848             1    1      1
  283982             1    1      1
  284361             1    1      0
  284371             0    1      1
  284498             1    1      1
  284521             1    1      1
  285346             1    1      1
  285362             1    1      1
  285498             1    1      1
  285555             1    1      1
  285834             1    1      0
  2859               1    1      1
  286                0    1      1
  286187             0    1      1
  286223             1    1      1
  286749             1    1      1
  287                1    1      1
  2873               1    1      1
  29058              1    1      1
  2914               0    1      1
  29850              0    1      1
  29914              1    1      1
  29990              1    1      1
  29998              1    1      1
  3012               0    1      1
  3017               0    1      1
  30820              0    1      1
  3084               1    1      1
  3164               1    1      1
  3172               1    1      1
  317703             1    1      0
  3187               1    1      0
  324                1    0      1
  3320               0    1      1
  3338               0    1      1
  338872             1    1      1
  338879             1    1      1
  339501             0    1      0
  339512             1    1      1
  339766             1    1      1
  340069             0    1      1
  340094             0    1      1
  340205             0    1      1
  340441             1    1      1
  340526             1    1      1
  340595             1    1      1
  341346             1    1      1
  342931             1    1      1
  343068             1    1      1
  3441               0    1      1
  344892             1    1      1
  345062             0    1      1
  347169             1    1      1
  347475             1    1      1
  348751             1    1      1
  353149             0    1      1
  3556               1    1      1
  3581               0    1      0
  359710             0    1      1
  359845             1    1      1
  360226             0    1      1
  3609               0    1      1
  3655               0    1      1
  3699               0    1      1
  3712               0    1      1
  373856             1    1      1
  3742               1    1      1
  374286             0    1      0
  374308             1    1      1
  374462             1    1      1
  374864             1    1      1
  374900             0    1      1
  374907             0    1      1
  374986             1    1      1
  375449             1    1      1
  375616             0    1      0
  375748             1    1      1
  375757             0    1      1
  3778               1    1      1
  3801               0    0      1
  3805               0    1      1
  3809               1    1      1
  3811               1    1      1
  3831               0    1      1
  387104             1    1      1
  387263             1    1      1
  387522             1    1      1
  387723             1    1      0
  388199             1    1      1
  388276             0    1      1
  388324             1    1      1
  388677             1    1      1
  388685             1    1      0
  388761             1    1      1
  388795             1    1      1
  388960             0    1      1
  389197             1    1      1
  389199             0    1      1
  389690             1    1      1
  389895             1    1      0
  390226             1    1      1
  390748             1    1      1
  390877             0    1      1
  391003             1    1      1
  392490             1    1      1
  392617             1    1      1
  3983               1    1      1
  400073             1    1      1
  400087             1    1      0
  400499             1    1      1
  400533             1    1      0
  400620             1    1      0
  400797             1    1      0
  400818             1    1      1
  400986             1    1      1
  401067             1    1      1
  401082             1    1      1
  401115             1    1      1
  401149             1    1      0
  401237             1    1      1
  401399             1    1      1
  401497             0    1      0
  401992             1    1      1
  401994             1    1      1
  402160             1    1      1
  4033               0    1      0
  403323             1    1      0
  403341             1    1      1
  404734             1    1      1
  407977             0    1      1
  408186             1    1      1
  414061             0    1      1
  4168               1    1      1
  4174               1    1      0
  433                0    1      1
  439915             0    1      1
  440348             1    1      1
  440352             1    1      1
  440353             1    1      1
  440556             1    1      1
  440689             1    1      1
  440896             1    1      0
  440993             1    1      1
  441108             0    0      1
  441155             1    1      1
  441239             0    1      0
  441251             1    1      1
  441452             1    1      1
  441459             1    1      1
  441525             1    1      1
  441631             1    1      0
  441669             1    1      0
  441911             1    1      1
  442179             1    1      0
  445347             1    1      1
  445372             0    1      1
  445815             1    1      1
  448834             1    1      1
  4583               1    1      1
  463                1    1      1
  4636               1    1      1
  474354             1    1      1
  4802               0    1      1
  4883               0    0      1
  493754             1    1      0
  493901             0    1      1
  4946               0    1      1
  4948               1    1      0
  4957               1    1      1
  4988               0    1      1
  4992               1    1      1
  4995               1    1      1
  503834             1    1      1
  50514              1    1      1
  50636              0    1      1
  50650              0    1      1
  5099               1    1      1
  51031              1    1      1
  51043              1    1      1
  51088              1    1      0
  51207              0    1      1
  51265              1    1      0
  51266              1    1      1
  51351              1    1      1
  5136               1    1      1
  5137               1    1      1
  5143               1    1      1
  51435              1    1      0
  5144               0    1      1
  51466              1    1      0
  5154               0    1      0
  51557              1    1      0
  51686              1    1      1
  5217               0    1      1
  5271               1    1      0
  5308               0    1      1
  5320               0    1      1
  53354              1    1      1
  5339               0    1      1
  53405              1    1      1
  53616              0    0      1
  53632              1    1      1
  54097              1    1      1
  5430               1    1      1
  54331              1    1      1
  54332              0    1      0
  5437               0    1      1
  54536              0    0      1
  54585              0    0      1
  5475               1    1      1
  54825              1    1      1
  548644             1    1      1
  54914              1    1      1
  5495               1    1      1
  54970              0    1      0
  54998              0    1      1
  55                 1    1      1
  55041              1    1      1
  55179              0    1      1
  5522               0    1      1
  55267              1    1      1
  5527               1    1      1
  55284              0    1      1
  552891             0    1      1
  55297              0    1      1
  553158             0    1      1
  55324              1    1      1
  55350              0    1      1
  55384              1    1      1
  55507              1    1      1
  55521              0    1      1
  55567              1    1      1
  55672              1    1      1
  55715              0    1      1
  55734              0    1      1
  55769              1    1      1
  55793              1    1      1
  55809              1    1      1
  55819              1    1      1
  55841              1    1      1
  55959              1    1      1
  55964              1    1      1
  56165              1    1      1
  56341              0    1      1
  5646               0    1      1
  56606              1    1      0
  56658              0    1      1
  56901              0    1      1
  56907              1    1      1
  56911              1    1      1
  56918              1    1      1
  56924              0    1      1
  56938              1    1      1
  56955              1    1      1
  5697               1    1      1
  56971              1    1      1
  56977              0    1      0
  57002              0    1      1
  57047              1    1      1
  57093              1    1      0
  57153              1    1      1
  57180              1    1      0
  5733               1    1      1
  57451              1    1      1
  57480              1    1      1
  57489              1    1      1
  57529              1    1      1
  57571              1    1      1
  57583              1    1      1
  57624              1    1      1
  57642              1    1      1
  57644              0    0      1
  57674              0    1      1
  57690              1    1      1
  57705              1    1      1
  57821              1    1      1
  57835              1    1      1
  5900               0    0      1
  5906               1    1      1
  5983               1    1      1
  5988               1    1      1
  5998               1    1      1
  6006               1    1      1
  60312              1    1      1
  60437              1    1      1
  60487              1    1      0
  60490              1    1      0
  60506              1    1      1
  6092               1    1      1
  6101               1    1      1
  613037             0    1      0
  613211             1    1      1
  613227             1    1      1
  6196               0    1      1
  6276               0    1      1
  631                1    1      1
  6370               0    1      1
  64067              1    1      1
  64097              1    1      1
  641517             1    1      1
  642484             1    1      1
  642515             0    1      1
  642612             1    1      1
  642799             0    1      0
  642819             1    1      1
  643311             0    1      1
  643314             0    1      1
  643376             1    1      1
  643382             1    1      1
  64342              1    1      0
  643723             1    1      0
  644100             1    1      1
  645191             1    1      1
  645202             1    1      1
  645369             1    1      1
  645414             1    1      1
  645425             1    1      1
  64582              1    1      1
  646262             1    1      1
  646588             1    1      0
  646915             1    1      0
  647264             1    1      0
  64756              0    1      1
  64770              1    1      1
  64860              0    1      1
  650226             1    1      0
  65109              0    1      0
  65249              0    1      0
  65265              0    1      0
  653061             1    1      1
  653149             1    1      1
  653857             1    1      0
  654231             1    1      1
  65982              0    0      1
  65983              0    1      1
  6675               0    1      1
  6698               1    1      1
  6733               1    1      0
  6757               0    0      1
  6788               1    1      1
  6867               0    1      1
  692312             0    1      1
  7005               1    1      1
  7037               1    1      1
  7082               0    1      1
  7089               0    1      1
  7182               0    1      1
  7275               1    1      1
  727800             0    1      1
  728194             1    1      0
  728392             1    1      1
  728441             1    1      1
  728588             1    1      1
  728763             1    1      1
  728888             1    1      1
  728957             1    1      1
  728989             1    1      1
  729218             1    1      0
  729262             0    1      0
  729359             1    1      1
  729428             1    1      1
  729767             0    1      1
  729978             1    1      1
  730005             0    0      1
  730098             1    1      1
  731275             1    1      1
  7402               1    1      1
  7417               0    1      1
  7422               1    0      1
  744                1    1      1
  7466               1    1      0
  7494               0    1      1
  7547               0    0      1
  7587               0    1      1
  7594               0    1      0
  7644               1    1      0
  767558             0    0      1
  7739               1    1      1
  7757               0    1      0
  7767               1    1      1
  777                0    1      0
  7771               0    1      1
  7775               1    1      1
  7798               1    1      1
  79015              1    1      0
  79020              1    1      1
  79037              0    1      1
  79081              0    1      1
  79091              1    1      0
  79470              1    1      1
  79589              0    1      1
  79676              1    1      1
  79750              1    1      0
  79784              0    1      0
  79917              0    1      1
  79921              0    1      1
  79931              0    1      1
  79949              0    1      1
  80036              0    0      1
  80095              1    1      1
  80125              1    1      1
  80254              0    1      1
  80728              1    1      1
  80741              0    1      1
  80817              1    1      1
  80833              1    1      1
  80854              0    1      1
  81328              1    1      1
  81458              1    1      1
  81889              0    1      1
  8225               0    1      1
  83259              1    1      1
  83463              0    1      1
  8347               1    1      1
  83551              0    1      1
  84253              0    0      1
  84309              1    1      1
  84337              0    1      1
  84460              0    1      1
  8453               0    1      0
  84614              1    1      1
  8470               1    1      1
  84725              0    1      1
  84750              1    1      0
  84765              1    1      1
  84790              0    1      1
  84808              1    1      1
  84851              1    1      1
  84876              0    1      1
  84924              1    1      1
  84985              1    1      1
  8525               1    1      1
  85358              1    1      1
  85395              0    1      1
  85397              1    1      1
  85439              1    1      1
  85441              1    1      1
  85452              1    1      1
  8638               0    1      0
  8668               0    1      1
  8681               1    1      1
  8711               0    1      1
  8785               1    1      1
  8801               0    1      1
  8857               1    1      1
  89780              1    1      0
  89795              0    1      1
  89796              1    1      1
  8996               0    1      1
  90007              1    1      1
  90019              1    1      1
  90050              1    1      1
  90113              1    1      1
  90293              1    1      1
  9033               1    1      0
  90362              1    1      1
  9038               1    1      1
  90416              1    1      1
  90417              0    1      1
  90523              1    1      0
  90850              1    1      1
  91227              0    1      0
  91526              0    1      0
  9154               1    1      1
  91544              1    1      1
  91646              1    1      1
  91833              1    1      1
  91869              1    1      0
  92292              1    1      1
  9274               0    1      1
  92806              1    1      1
  92949              0    1      0
  93594              1    1      0
  94025              1    1      0
  94121              1    1      1
  9425               0    1      1
  9478               1    1      1
  9498               0    1      1
  9534               1    1      0
  9612               1    1      1
  9628               1    1      0
  9645               1    1      1
  9651               1    1      1
  9686               1    1      1
  9693               1    1      1
  9721               1    1      1
  9734               1    1      1
  9738               1    1      1
  9745               1    1      0
  9758               0    1      0
  9887               1    1      1
  9906               1    1      1
  9922               0    1      0
  9942               1    1      0
  9994               1    1      1
  ENSG00000112096    1    1      1
  ENSG00000182230    1    1      1
  ENSG00000215271    1    1      1
  ENSG00000221995    1    1      1
  ENSG00000249860    1    1      1
  ENSG00000256045    1    1      1
  ENSG00000256222    1    1      1
  ENSG00000256892    1    1      0
  ENSG00000269028    1    1      0
  ENSG00000270188    1    1      0
  ENSG00000270394    1    1      0
# Display samples in removed ENSEMBL IDs that are in PMTL list
filtered_ensg %>% dplyr::filter(Ensembl_ID %in% pmtl_ids) %>% 
  select(Ensembl_ID, Kids_First_Biospecimen_ID) %>% 
  dplyr::distinct()
# Remove data frames
rm(variant_level_snv, filtered_ensg, consensus_ensg)

Gene level CNV frequencies

# read mtp table
mtp_file <- 
  file.path(input_dir, "gene-level-cnv-consensus-annotated-mut-freq.tsv.gz")
gene_level_cnv <- 
  data.table::fread(mtp_file, sep = "\t", showProgress = FALSE) %>%
    tibble::as_tibble() 
# filter mtp table 
file_name <- basename(mtp_file)
filter_mtp_table(gene_level_cnv, ensg_ids, file_name)  
# Ensembl gene identifiers removed
filtered_ensg <- gene_level_cnv %>% 
  dplyr::filter(!targetFromSourceId %in% ensg_ids) %>% 
  dplyr::select(Gene_symbol, targetFromSourceId) %>%
  dplyr::rename(Ensembl_ID = targetFromSourceId) %>% 
  dplyr::distinct()

# read the CNV consensus file
consensus_ensg <- data.table::fread(
  file.path(data_dir, "consensus_wgs_plus_cnvkit_wxs.tsv.gz"), 
  select = c("biospecimen_id", "ensembl"), showProgress = FALSE) %>% 
  tibble::as_tibble() %>% 
  dplyr::filter(!is.na(ensembl)) %>% 
  dplyr::rename(Kids_First_Biospecimen_ID = biospecimen_id) %>% 
  dplyr::distinct()

# merge sample IDs to filtered OT ENSG IDs
filtered_ensg <- filtered_ensg %>% 
  dplyr::left_join(consensus_ensg, by=c("Ensembl_ID" = "ensembl"))

# merge OpenPedCan cohorts to filtered OT ENSG IDs
filtered_ensg <- filtered_ensg %>% 
  dplyr::left_join(sample_ids, by= "Kids_First_Biospecimen_ID")

# write to file
readr::write_tsv(filtered_ensg,
  file.path(results_dir, 
            "gene-level-cnv-consensus-annotated-mut-freq_dropped_ensg.tsv.gz"))

# Display removed ENSEMBL IDs 
filtered_ensg %>% dplyr::select(Ensembl_ID, cohort) %>% 
  dplyr::distinct() %>%
  tidyr::drop_na() %>% 
  table()
                 cohort
Ensembl_ID        GMKF PBTA TARGET
  ENSG00000112096    1    1      1
  ENSG00000161149    1    1      1
  ENSG00000182230    1    1      1
  ENSG00000215271    1    1      1
  ENSG00000221995    1    1      1
  ENSG00000228139    1    1      1
  ENSG00000232196    1    1      1
  ENSG00000233776    1    1      1
  ENSG00000249860    1    1      1
  ENSG00000255823    1    1      1
  ENSG00000256045    1    1      1
  ENSG00000256222    1    1      1
  ENSG00000256618    1    1      1
  ENSG00000256892    1    1      1
  ENSG00000258808    1    1      1
  ENSG00000258861    1    1      1
  ENSG00000261737    1    1      1
  ENSG00000269900    1    1      1
  ENSG00000270672    1    1      1
  ENSG00000273888    1    1      1
  ENSG00000283486    1    1      1
# Display samples in removed ENSEMBL IDs that are in PMTL list
filtered_ensg %>% dplyr::filter(Ensembl_ID %in% pmtl_ids) %>% 
  select(Ensembl_ID, Kids_First_Biospecimen_ID) %>% 
  dplyr::distinct()
# Remove data frames
rm(gene_level_cnv, filtered_ensg, consensus_ensg)

Fusion frequencies

# read mtp table
mtp_file <- file.path(input_dir, "putative-oncogene-fusion-freq.tsv.gz")
fusion <- 
  data.table::fread(mtp_file, sep = "\t", showProgress = FALSE) %>%
    tibble::as_tibble() 
# filter mtp table 
file_name <- basename(mtp_file)
filter_mtp_table(fusion, ensg_ids, file_name) 
# Ensembl gene identifiers removed
filtered_ensg <- fusion %>% 
  dplyr::filter(!targetFromSourceId %in% ensg_ids) %>% 
  dplyr::select(FusionName, Gene_symbol, targetFromSourceId) %>%
  dplyr::rename(Ensembl_ID = targetFromSourceId) %>% 
  dplyr::distinct()

# split fusion name into constituent genes  symbols
fusion_names <- data.table::fread(
  file.path(data_dir, "fusion-putative-oncogenic.tsv"), 
  select = c("Sample", "FusionName"), showProgress = FALSE) %>% 
  tibble::as_tibble() %>% 
  tidyr::separate_rows(FusionName, sep = "--", convert = FALSE) %>% 
  tidyr::separate_rows(FusionName, sep = '/', convert = FALSE) %>% 
  dplyr::rename(Kids_First_Biospecimen_ID = Sample, 
                Gene_symbol = FusionName) %>% 
  dplyr::filter(!is.na(Gene_symbol)) %>% 
  dplyr::distinct() 

# merge sample IDs to filtered OT ENSG IDs
filtered_ensg <- filtered_ensg %>% 
  dplyr::left_join(fusion_names, by="Gene_symbol") %>% 
  dplyr::select(-FusionName) %>% 
  dplyr::distinct()

# merge OpenPedCan cohorts to filtered OT ENSG IDs
filtered_ensg <- filtered_ensg %>% 
  dplyr::left_join(sample_ids, by = "Kids_First_Biospecimen_ID")

# write to file
readr::write_tsv(filtered_ensg,
  file.path(results_dir, 
            "putative-oncogene-fusion-freq_dropped_ensg.tsv.gz"))

# Display removed ENSEMBL IDs 
filtered_ensg %>% dplyr::select(Ensembl_ID, cohort) %>% 
  dplyr::distinct() %>%
  tidyr::drop_na() %>% 
  table()
                 cohort
Ensembl_ID        GMKF PBTA TARGET
                     0    1      1
  ENSG00000112096    0    1      1
  ENSG00000137808    0    0      1
  ENSG00000215271    0    0      1
  ENSG00000224739    0    0      1
  ENSG00000226380    0    1      1
  ENSG00000251044    0    1      0
  ENSG00000255633    0    0      1
  ENSG00000261737    0    1      0
  ENSG00000269028    0    0      1
  ENSG00000269900    0    1      1
  ENSG00000273301    0    1      0
  ENSG00000273730    0    1      1
  ENSG00000274202    0    1      0
  ENSG00000275405    0    0      1
  ENSG00000275757    0    1      1
  ENSG00000275987    0    0      1
  ENSG00000276345    0    0      1
  ENSG00000276612    0    0      1
  ENSG00000276711    0    1      0
  ENSG00000276932    1    1      1
  ENSG00000277374    0    0      1
  ENSG00000277428    1    1      1
  ENSG00000277890    1    1      1
  ENSG00000277927    1    1      1
  ENSG00000278294    0    1      1
  ENSG00000278457    0    1      0
  ENSG00000278625    1    1      1
  ENSG00000278793    1    1      1
  ENSG00000279765    0    0      1
  ENSG00000282965    0    1      0
  ENSG00000284299    0    1      0
  ENSG00000285106    1    1      1
  ENSG00000285762    1    1      0
  ENSG00000288884    0    0      1
  ENSG00000289638    0    0      1
# Display samples in removed ENSEMBL IDs that are in PMTL list
filtered_ensg %>% dplyr::filter(Ensembl_ID %in% pmtl_ids) %>% 
  select(Ensembl_ID, Kids_First_Biospecimen_ID) %>% 
  dplyr::distinct()
# Remove frequencies data frame
rm(fusion, filtered_ensg)

Fused gene frequencies

# read mtp table
mtp_file <- file.path(input_dir, "putative-oncogene-fused-gene-freq.tsv.gz")
fused_gene <- 
  data.table::fread(mtp_file, sep = "\t", showProgress = FALSE) %>%
    tibble::as_tibble() 
# filter mtp table 
file_name <- basename(mtp_file)
filter_mtp_table(fused_gene, ensg_ids, file_name)
# Ensembl gene identifiers removed
filtered_ensg <- fused_gene %>% 
  dplyr::filter(!targetFromSourceId %in% ensg_ids) %>% 
  dplyr::select(Gene_symbol, targetFromSourceId) %>%
  dplyr::rename(Ensembl_ID = targetFromSourceId) %>% 
  dplyr::distinct()

# merge sample IDs to filtered OT ENSG IDs
filtered_ensg <- filtered_ensg %>% 
  dplyr::left_join(fusion_names, by = "Gene_symbol") %>% 
  dplyr::distinct()

# merge sample IDs to filtered OT ENSG IDs
filtered_ensg <- filtered_ensg %>% 
  dplyr::left_join(sample_ids, by = "Kids_First_Biospecimen_ID")

# write to file
readr::write_tsv(filtered_ensg,
  file.path(results_dir, 
            "putative-oncogene-fused-gene-freq_dropped_ensg.tsv.gz"))

# Display removed ENSEMBL IDs 
filtered_ensg %>% dplyr::select(Ensembl_ID, cohort) %>% 
  dplyr::distinct() %>%
  tidyr::drop_na() %>% 
  table()
                 cohort
Ensembl_ID        GMKF PBTA TARGET
                     0    1      1
  ENSG00000112096    0    1      1
  ENSG00000137808    0    0      1
  ENSG00000215271    0    0      1
  ENSG00000224739    0    0      1
  ENSG00000226380    0    1      1
  ENSG00000251044    0    1      0
  ENSG00000255633    0    0      1
  ENSG00000261737    0    1      0
  ENSG00000269028    0    0      1
  ENSG00000269900    0    1      1
  ENSG00000273301    0    1      0
  ENSG00000273730    0    1      1
  ENSG00000274202    0    1      0
  ENSG00000275405    0    0      1
  ENSG00000275757    0    1      1
  ENSG00000275987    0    0      1
  ENSG00000276345    0    0      1
  ENSG00000276612    0    0      1
  ENSG00000276711    0    1      0
  ENSG00000276932    1    1      1
  ENSG00000277374    0    0      1
  ENSG00000277428    1    1      1
  ENSG00000277890    1    1      1
  ENSG00000277927    1    1      1
  ENSG00000278294    0    1      1
  ENSG00000278457    0    1      0
  ENSG00000278625    1    1      1
  ENSG00000278793    1    1      1
  ENSG00000279765    0    0      1
  ENSG00000282965    0    1      0
  ENSG00000284299    0    1      0
  ENSG00000285106    1    1      1
  ENSG00000285762    1    1      0
  ENSG00000288884    0    0      1
  ENSG00000289638    0    0      1
# Display samples in removed ENSEMBL IDs that are in PMTL list
filtered_ensg %>% dplyr::filter(Ensembl_ID %in% pmtl_ids) %>% 
  select(Ensembl_ID, Kids_First_Biospecimen_ID) %>% 
  dplyr::distinct()
# Remove frequencies data frame
rm(fused_gene, filtered_ensg, fusion_names)

Gene expression TPM group-wise summary statistics

OpenPedCan collapsed gene expressions TPM matrix only contains gene symbols and not ENSEMBL gene identifiers. Therefore, samples associated with removed ENSEMBL identifiers cannot be listed.

# read mtp table
mtp_file <- 
  file.path(input_dir, "long_n_tpm_mean_sd_quantile_group_wise_zscore.tsv.gz")
tpm_group_wise_stats <- 
  data.table::fread(mtp_file, sep = "\t", showProgress = FALSE) %>%
    tibble::as_tibble() 
# filter mtp table 
file_name <- basename(mtp_file)
filter_mtp_table(tpm_group_wise_stats, ensg_ids, file_name)
# Ensembl gene identifiers removed
filtered_ensg <- tpm_group_wise_stats %>% 
  dplyr::filter(!Gene_Ensembl_ID %in% ensg_ids) %>% 
  dplyr::select(Gene_symbol, Gene_Ensembl_ID, cohort) %>%
  dplyr::rename(Ensembl_ID = Gene_Ensembl_ID) %>% 
  dplyr::distinct()

# write to file
readr::write_tsv(filtered_ensg,
  file.path(results_dir, 
            "long_n_tpm_mean_sd_quantile_group_wise_zscore_dropped_ensg.tsv.gz"))

# Display removed ENSEMBL IDs 
filtered_ensg %>% dplyr::select(Ensembl_ID, cohort) %>% 
  dplyr::filter(cohort != "All Cohorts") %>% 
  dplyr::distinct() %>%
  tidyr::drop_na() %>%  
  table()
                 cohort
Ensembl_ID        GMKF PBTA TARGET TCGA
  ENSG00000112096    1    1      1    1
  ENSG00000204092    1    1      1    1
  ENSG00000212951    1    1      1    1
  ENSG00000215271    1    1      1    1
  ENSG00000221995    1    1      1    1
  ENSG00000224739    1    1      1    1
  ENSG00000226377    1    1      1    1
  ENSG00000226380    1    1      1    1
  ENSG00000227021    1    1      1    1
  ENSG00000227220    1    1      1    1
  ENSG00000227902    1    1      1    1
  ENSG00000228139    1    1      1    1
  ENSG00000228206    1    1      1    1
  ENSG00000228906    1    1      1    1
  ENSG00000229352    1    1      1    1
  ENSG00000232196    1    1      1    1
  ENSG00000233776    1    1      1    1
  ENSG00000236166    1    1      1    1
  ENSG00000236673    1    1      1    1
  ENSG00000236886    1    1      1    1
  ENSG00000239467    1    1      1    1
  ENSG00000239665    1    1      1    1
  ENSG00000249860    1    1      1    1
  ENSG00000251044    1    1      1    1
  ENSG00000253878    1    1      1    1
  ENSG00000254561    1    1      1    1
  ENSG00000254740    1    1      1    1
  ENSG00000255633    1    1      1    1
  ENSG00000255823    1    1      1    1
  ENSG00000256045    1    1      1    1
  ENSG00000256222    1    1      1    1
  ENSG00000256427    1    1      1    1
  ENSG00000256618    1    1      1    1
  ENSG00000256892    1    1      1    1
  ENSG00000258414    1    1      1    1
  ENSG00000258808    1    1      1    1
  ENSG00000258861    1    1      1    1
  ENSG00000259834    1    1      1    1
  ENSG00000259855    1    1      1    1
  ENSG00000260461    1    1      1    1
  ENSG00000261068    1    1      1    1
  ENSG00000261490    1    1      1    1
  ENSG00000261773    1    1      1    1
  ENSG00000269028    1    1      1    1
  ENSG00000270188    1    1      1    1
  ENSG00000270394    1    1      1    1
  ENSG00000270672    1    1      1    1
  ENSG00000271043    1    1      1    1
  ENSG00000271409    1    1      1    1
  ENSG00000271734    1    1      1    1
  ENSG00000271870    1    1      1    1
  ENSG00000272551    1    1      1    1
  ENSG00000272567    1    1      1    1
  ENSG00000272880    1    1      1    1
  ENSG00000273301    1    1      1    1
  ENSG00000273614    1    1      1    1
  ENSG00000273837    1    1      1    1
  ENSG00000273888    1    1      1    1
  ENSG00000273923    1    1      1    1
  ENSG00000277050    1    1      1    1
  ENSG00000277352    1    1      1    1
  ENSG00000278927    1    1      1    1
  ENSG00000278955    1    1      1    1
  ENSG00000279226    1    1      1    1
  ENSG00000279769    1    1      1    1
  ENSG00000279948    1    1      1    1
  ENSG00000280058    1    1      1    1
  ENSG00000280095    1    1      1    1
  ENSG00000280346    1    1      1    1
  ENSG00000280374    1    1      1    1
  ENSG00000282965    1    1      1    1
# Remove summary statistics data frame
rm(tpm_group_wise_stats, filtered_ensg)

Gene expression TPM gene-wise summary statistics

OpenPedCan collapsed gene expressions TPM matrix only contains gene symbols and not ENSEMBL gene identifiers. Therefore, samples associated with removed ENSEMBL identifiers cannot be listed.

# read mtp table
mtp_file <- 
  file.path(input_dir, "long_n_tpm_mean_sd_quantile_gene_wise_zscore.tsv.gz")
tpm_gene_wise_stats <- 
  data.table::fread(mtp_file, sep = "\t", showProgress = FALSE) %>%
    tibble::as_tibble() 
# filter mtp table 
file_name <- basename(mtp_file)
filter_mtp_table(tpm_gene_wise_stats, ensg_ids, file_name)
# Ensembl gene identifiers removed
filtered_ensg <- tpm_gene_wise_stats %>% 
  dplyr::filter(!Gene_Ensembl_ID %in% ensg_ids) %>% 
  dplyr::select(Gene_symbol, Gene_Ensembl_ID, cohort) %>%
  dplyr::rename(Ensembl_ID = Gene_Ensembl_ID) %>% 
  dplyr::distinct()

# write to file
readr::write_tsv(filtered_ensg,
  file.path(results_dir, 
            "long_n_tpm_mean_sd_quantile_gene_wise_zscore_dropped_ensg.tsv.gz"))

# Display removed ENSEMBL IDs 
filtered_ensg %>% dplyr::select(Ensembl_ID, cohort) %>% 
  dplyr::filter(cohort != "All Cohorts") %>% 
  dplyr::distinct() %>%
  tidyr::drop_na() %>%  
  table()
                 cohort
Ensembl_ID        GMKF PBTA TARGET TCGA
  ENSG00000112096    1    1      1    1
  ENSG00000204092    1    1      1    1
  ENSG00000212951    1    1      1    1
  ENSG00000215271    1    1      1    1
  ENSG00000221995    1    1      1    1
  ENSG00000224739    1    1      1    1
  ENSG00000226377    1    1      1    1
  ENSG00000226380    1    1      1    1
  ENSG00000227021    1    1      1    1
  ENSG00000227220    1    1      1    1
  ENSG00000227902    1    1      1    1
  ENSG00000228139    1    1      1    1
  ENSG00000228206    1    1      1    1
  ENSG00000228906    1    1      1    1
  ENSG00000229352    1    1      1    1
  ENSG00000232196    1    1      1    1
  ENSG00000233776    1    1      1    1
  ENSG00000236166    1    1      1    1
  ENSG00000236673    1    1      1    1
  ENSG00000236886    1    1      1    1
  ENSG00000239467    1    1      1    1
  ENSG00000239665    1    1      1    1
  ENSG00000249860    1    1      1    1
  ENSG00000251044    1    1      1    1
  ENSG00000253878    1    1      1    1
  ENSG00000254561    1    1      1    1
  ENSG00000254740    1    1      1    1
  ENSG00000255633    1    1      1    1
  ENSG00000255823    1    1      1    1
  ENSG00000256045    1    1      1    1
  ENSG00000256222    1    1      1    1
  ENSG00000256427    1    1      1    1
  ENSG00000256618    1    1      1    1
  ENSG00000256892    1    1      1    1
  ENSG00000258414    1    1      1    1
  ENSG00000258808    1    1      1    1
  ENSG00000258861    1    1      1    1
  ENSG00000259834    1    1      1    1
  ENSG00000259855    1    1      1    1
  ENSG00000260461    1    1      1    1
  ENSG00000261068    1    1      1    1
  ENSG00000261490    1    1      1    1
  ENSG00000261773    1    1      1    1
  ENSG00000269028    1    1      1    1
  ENSG00000270188    1    1      1    1
  ENSG00000270394    1    1      1    1
  ENSG00000270672    1    1      1    1
  ENSG00000271043    1    1      1    1
  ENSG00000271409    1    1      1    1
  ENSG00000271734    1    1      1    1
  ENSG00000271870    1    1      1    1
  ENSG00000272551    1    1      1    1
  ENSG00000272567    1    1      1    1
  ENSG00000272880    1    1      1    1
  ENSG00000273301    1    1      1    1
  ENSG00000273614    1    1      1    1
  ENSG00000273837    1    1      1    1
  ENSG00000273888    1    1      1    1
  ENSG00000273923    1    1      1    1
  ENSG00000277050    1    1      1    1
  ENSG00000277352    1    1      1    1
  ENSG00000278927    1    1      1    1
  ENSG00000278955    1    1      1    1
  ENSG00000279226    1    1      1    1
  ENSG00000279769    1    1      1    1
  ENSG00000279948    1    1      1    1
  ENSG00000280058    1    1      1    1
  ENSG00000280095    1    1      1    1
  ENSG00000280346    1    1      1    1
  ENSG00000280374    1    1      1    1
  ENSG00000282965    1    1      1    1
# Remove summary statistics data frame
rm(tpm_gene_wise_stats, filtered_ensg)

Methylation gene-level summary

OpenPedCan contains methylation and rnaseq summaries of cohort cancer groups and can’t not associate with samples. Therefore, samples associated with removed ENSEMBL identifiers cannot be listed.

# read mtp table
mtp_file <- file.path(input_dir, "gene-methyl-beta-values-summary.tsv.gz")
gene_level_methyl <- 
  data.table::fread(mtp_file, sep = "\t", showProgress = FALSE) %>%
    tibble::as_tibble() 
# filter mtp table 
file_name <- basename(mtp_file)
filter_mtp_table(gene_level_methyl, ensg_ids, file_name)
# Ensembl gene identifiers removed
filtered_ensg <- gene_level_methyl %>% 
  dplyr::filter(!targetFromSourceId %in% ensg_ids) %>% 
  dplyr::select(Gene_symbol, targetFromSourceId, Dataset) %>%
  dplyr::rename(Ensembl_ID = targetFromSourceId, cohort = Dataset) %>% 
  dplyr::distinct()

# write to file
readr::write_tsv(filtered_ensg,
  file.path(results_dir, 
            "gene-methyl-beta-values-summary_dropped_ensg.tsv.gz"))

# Display removed ENSEMBL IDs 
filtered_ensg %>% dplyr::select(Ensembl_ID, cohort) %>% 
  dplyr::distinct() %>%
  tidyr::drop_na() %>% 
  table()
                 cohort
Ensembl_ID        PBTA TARGET
                     1      1
  ENSG00000112096    1      1
  ENSG00000204092    1      0
  ENSG00000212951    1      0
  ENSG00000215271    1      1
  ENSG00000221995    1      1
  ENSG00000224739    1      1
  ENSG00000226377    1      1
  ENSG00000226380    1      1
  ENSG00000227021    1      1
  ENSG00000227220    1      1
  ENSG00000229352    1      1
  ENSG00000232196    1      1
  ENSG00000236166    1      1
  ENSG00000236673    1      1
  ENSG00000236886    1      1
  ENSG00000239467    1      1
  ENSG00000239665    1      1
  ENSG00000249860    1      0
  ENSG00000253878    1      1
  ENSG00000254561    1      1
  ENSG00000254740    1      1
  ENSG00000255823    1      1
  ENSG00000256222    1      1
  ENSG00000256427    1      1
  ENSG00000256618    1      1
  ENSG00000256892    1      0
  ENSG00000258414    1      0
  ENSG00000258808    1      1
  ENSG00000258861    1      1
  ENSG00000261068    1      0
  ENSG00000269900    1      1
  ENSG00000270394    1      1
  ENSG00000270672    1      1
  ENSG00000273888    1      1
  ENSG00000279948    1      0
  ENSG00000282965    1      1
# Remove frequencies data frame
rm(gene_level_methyl, filtered_ensg)

Methylation gene-level summary

OpenPedCan contains methylation and rnaseq summaries of cohort cancer groups and can’t not associate with samples. Therefore, samples associated with removed ENSEMBL identifiers cannot be listed.

# read mtp table
mtp_file <- file.path(input_dir, "isoform-methyl-beta-values-summary.tsv.gz")
isoform_level_methyl <- 
  data.table::fread(mtp_file, sep = "\t", showProgress = FALSE) %>%
    tibble::as_tibble() 
# filter mtp table 
file_name <- basename(mtp_file)
filter_mtp_table(isoform_level_methyl, ensg_ids, file_name)
# Ensembl gene identifiers removed
filtered_ensg <- isoform_level_methyl %>% 
  dplyr::filter(!targetFromSourceId %in% ensg_ids) %>% 
  dplyr::select(Gene_symbol, targetFromSourceId, Dataset) %>%
  dplyr::rename(Ensembl_ID = targetFromSourceId, cohort = Dataset) %>% 
  dplyr::distinct()

# write to file
readr::write_tsv(filtered_ensg,
  file.path(results_dir, 
            "isoform-methyl-beta-values-summary_dropped_ensg.tsv.gz"))

# Display removed ENSEMBL IDs 
filtered_ensg %>% dplyr::select(Ensembl_ID, cohort) %>% 
  dplyr::distinct() %>%
  tidyr::drop_na() %>% 
  table()
                 cohort
Ensembl_ID        PBTA TARGET
                     1      1
  ENSG00000112096    1      1
  ENSG00000137808    1      1
  ENSG00000161149    1      1
  ENSG00000182230    1      1
  ENSG00000204092    1      0
  ENSG00000212951    1      0
  ENSG00000215271    1      1
  ENSG00000221995    1      1
  ENSG00000224739    1      1
  ENSG00000226377    1      1
  ENSG00000226380    1      1
  ENSG00000227021    1      1
  ENSG00000227220    1      1
  ENSG00000229352    1      1
  ENSG00000232196    1      1
  ENSG00000236166    1      1
  ENSG00000236673    1      1
  ENSG00000236886    1      1
  ENSG00000239446    1      1
  ENSG00000239467    1      1
  ENSG00000239665    1      1
  ENSG00000249860    1      0
  ENSG00000253878    1      1
  ENSG00000254561    1      1
  ENSG00000254740    1      1
  ENSG00000255823    1      1
  ENSG00000256222    1      1
  ENSG00000256427    1      1
  ENSG00000256618    1      1
  ENSG00000256892    1      0
  ENSG00000258414    1      0
  ENSG00000258808    1      1
  ENSG00000258861    1      1
  ENSG00000261068    1      0
  ENSG00000261737    1      1
  ENSG00000269900    1      1
  ENSG00000270394    1      1
  ENSG00000270672    1      1
  ENSG00000272904    1      1
  ENSG00000273888    1      1
  ENSG00000279765    1      1
  ENSG00000279948    1      0
  ENSG00000282246    1      1
  ENSG00000282965    1      1
  ENSG00000283486    1      1
  ENSG00000284299    1      1
  ENSG00000285106    1      1
  ENSG00000285476    1      1
  ENSG00000285762    1      1
  ENSG00000286601    1      1
  ENSG00000286996    1      1
  ENSG00000287116    1      1
  ENSG00000288541    1      0
  ENSG00000288686    1      1
  ENSG00000288847    1      1
  ENSG00000288870    1      1
  ENSG00000288943    1      1
  ENSG00000288981    1      1
  ENSG00000289638    1      1
# Remove frequencies data frame
rm(isoform_level_methyl, filtered_ensg)

Session Info

sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 9 (stretch)

Matrix products: default
BLAS/LAPACK: /usr/lib/libopenblasp-r0.2.19.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=C             
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] jsonlite_1.6         data.table_1.12.2    forcats_0.4.0       
 [4] stringr_1.4.0        dplyr_0.8.3          purrr_0.3.2         
 [7] readr_1.3.1          tidyr_0.8.3          tibble_2.1.3        
[10] ggplot2_3.2.0        tidyverse_1.2.1      rtracklayer_1.46.0  
[13] GenomicRanges_1.38.0 GenomeInfoDb_1.22.1  IRanges_2.20.2      
[16] S4Vectors_0.24.4     BiocGenerics_0.32.0 

loaded via a namespace (and not attached):
 [1] Biobase_2.46.0              httr_1.4.0                 
 [3] R.utils_2.9.0               modelr_0.1.4               
 [5] assertthat_0.2.1            GenomeInfoDbData_1.2.2     
 [7] cellranger_1.1.0            Rsamtools_2.2.3            
 [9] yaml_2.2.0                  pillar_1.4.2               
[11] backports_1.1.4             lattice_0.20-38            
[13] glue_1.3.1                  digest_0.6.20              
[15] XVector_0.26.0              rvest_0.3.4                
[17] colorspace_1.4-1            htmltools_0.3.6            
[19] Matrix_1.2-17               R.oo_1.22.0                
[21] XML_3.98-1.20               pkgconfig_2.0.2            
[23] broom_0.5.2                 haven_2.1.1                
[25] zlibbioc_1.32.0             scales_1.0.0               
[27] BiocParallel_1.20.1         generics_0.0.2             
[29] withr_2.1.2                 SummarizedExperiment_1.16.1
[31] lazyeval_0.2.2              cli_1.1.0                  
[33] magrittr_1.5                crayon_1.3.4               
[35] readxl_1.3.1                evaluate_0.14              
[37] R.methodsS3_1.7.1           nlme_3.1-140               
[39] xml2_1.2.0                  tools_3.6.0                
[41] hms_0.4.2                   matrixStats_0.54.0         
[43] munsell_0.5.0               DelayedArray_0.12.3        
[45] Biostrings_2.54.0           compiler_3.6.0             
[47] rlang_0.4.0                 grid_3.6.0                 
[49] RCurl_1.95-4.12             rstudioapi_0.10            
[51] bitops_1.0-6                base64enc_0.1-3            
[53] rmarkdown_1.13              gtable_0.3.0               
[55] R6_2.4.0                    GenomicAlignments_1.22.1   
[57] lubridate_1.7.4             knitr_1.23                 
[59] rprojroot_1.3-2             stringi_1.4.3              
[61] Rcpp_1.0.1                  tidyselect_0.2.5           
[63] xfun_0.8                   
---
title: "Filter MTP Tables"
output: 
  html_notebook:
    toc: TRUE
    toc_float: TRUE
    toc_depth: 4
author: Eric Wafula, Sangeeta Shukla for Pediatric OpenTargets
date: 01/10/2021
---

Purpose: Remove Ensembl (ESNG) gene identifier in the mutation frequency tables, including SNV, CNV and fusion, TPM summary statistics and methylation summary tables that are not in Open Targets target list, and updated to match Open Target disease list.


## Usage

To run this from the command line, use:
```
Rscript -e "rmarkdown::render('01-filter-mtp-tables-for-current-gencode.Rmd', clean = TRUE)"
```
_This assumes you are in the modules directory of the repository, OpenPedCan-analysis/analyses/filter-mutation-frequency-tables._

## Setup

Load libraries
```{r}
# R analysis packages
suppressWarnings(
  suppressPackageStartupMessages(library(rtracklayer))
)
suppressPackageStartupMessages(library(tidyverse))
suppressPackageStartupMessages(library(data.table))
suppressPackageStartupMessages(library(jsonlite))

# Magrittr pipe
`%>%` <- dplyr::`%>%`
```


Set up directories. 
```{r}
# directories for input and output files
root_dir <- rprojroot::find_root(rprojroot::has_dir(".git"))
data_dir <- file.path(root_dir, "data")
scratch_dir <- file.path(root_dir, "scratch")
analyses_dir <- file.path(root_dir, "analyses")
module_dir <- file.path(analyses_dir, "filter-mtp-tables")
mtp_annot_results_dir <- file.path(analyses_dir,  "mtp-annotations/results")
gene_match_input_dir <- file.path(analyses_dir,  "gene_match/input")
input_dir <- file.path(scratch_dir,  "mtp-commit")
output_dir <- file.path(scratch_dir,  "mtp-filtered")
results_dir <- file.path(module_dir, "results")

# Create results folder if it doesn't exist
if (!dir.exists(results_dir)) {
  dir.create(results_dir)
}
```

## Get input data

Get Open Targets GENCODE Ensembl identifiers
```{r}
# filter for gene rows and get ids
ensg_ids <- readr::read_tsv(file.path(mtp_annot_results_dir, 
                                      "mtp-targets-mapping.tsv.gz")) %>% 
  dplyr::pull(gene_id) %>% 
  unique() 
```

Get PMTL Ensembl identifiers
```{r}
# filter for gene rows and get ids
pmtl_ids <- readr::read_tsv(file.path(gene_match_input_dir, "PMTL_v3.1.tsv")) %>% 
  dplyr::filter(Ensembl_ID != "Symbol_Not_Found") %>% 
  dplyr::pull(Ensembl_ID) %>% 
  unique() 
```

Get OpenPedCan sample IDs (Kids_First_Biospecimen_ID)
```{r}
sample_ids <- readr::read_tsv(file.path(data_dir, "histologies.tsv"), 
                              guess_max = 10000) %>% 
  dplyr::filter(sample_type == "Tumor") %>% 
  dplyr::select(Kids_First_Biospecimen_ID, cohort)
```

## Filter mutation frequencies tables

Function to filter for required Ensembl gene identifiers and write to file
```{r}

filter_mtp_table <- function(mtp_table, ensg_ids, file_name) {
  if ("Gene_Ensembl_ID" %in% colnames(mtp_table)) { 
    # filter mtp table and write to file
    mtp_table <- mtp_table %>%
      dplyr::filter(Gene_Ensembl_ID %in% ensg_ids) %>%
      dplyr::mutate(EFO = 
                      case_when(Disease == "Chordoma" ~ "MONDO_0008978",
                                Disease == "Meningioma" ~ "MONDO_0016642",
                                Disease == "Perineuroma" ~ "MONDO_0019404",
                                Disease == "Wilms tumor" ~ "MONDO_0006058",
                                TRUE ~ EFO)) %>% 
      dplyr::mutate(MONDO = 
                      case_when(Disease == "Perineuroma" ~ "MONDO_0019404",
                                TRUE ~ MONDO)) %>% 
      readr::write_tsv(file.path(output_dir, file_name))
  } else {
    # filter tsv mtp table
    mtp_table <- mtp_table %>% 
      dplyr::filter(targetFromSourceId %in% ensg_ids) %>%
      dplyr::mutate(diseaseFromSourceMappedId = 
                      case_when(Disease == "Chordoma" ~ "MONDO_0008978",
                                Disease == "Meningioma" ~ "MONDO_0016642",
                                Disease == "Perineuroma" ~ "MONDO_0019404",
                                Disease == "Wilms tumor" ~ "MONDO_0006058", 
                                TRUE ~ diseaseFromSourceMappedId)) %>% 
      dplyr::mutate(MONDO = 
                      case_when(Disease == "Perineuroma" ~ "MONDO_0019404",
                                TRUE ~ MONDO)) %>% 
      readr::write_tsv(file.path(output_dir, file_name))
     if (grepl("methyl", file_name)) {
       rds_file <- paste(unlist(str_split(file_name, "\\."))[1], "rds", sep = ".")
       mtp_table %>% readr::write_rds(file.path(output_dir, rds_file), compress = "gz")
     }
  }
return(mtp_table)
}
```

#### Gene level SNV frequencies
```{r}
# read mtp table
mtp_file <- 
  file.path(input_dir, "gene-level-snv-consensus-annotated-mut-freq.tsv.gz")
gene_level_snv <- 
  data.table::fread(mtp_file, sep = "\t", showProgress = FALSE) %>%
    tibble::as_tibble() 
# filter mtp table 
file_name <- basename(mtp_file)
filter_mtp_table(gene_level_snv, ensg_ids, file_name) 

# Ensembl gene identifiers removed
filtered_ensg <- gene_level_snv %>% 
  dplyr::filter(!targetFromSourceId %in% ensg_ids) %>% 
  dplyr::select(Gene_symbol, targetFromSourceId) %>%
  dplyr::rename(Ensembl_ID = targetFromSourceId) %>% 
  dplyr::distinct()

# read the SNV consensus file
consensus_ensg <- data.table::fread(
  file.path(data_dir, "snv-consensus-plus-hotspots.maf.tsv.gz"), 
  select = c("Tumor_Sample_Barcode", "Gene"), showProgress = FALSE) %>% 
  tibble::as_tibble() %>% 
  dplyr::filter(!is.na(Gene)) %>% 
  dplyr::rename(Kids_First_Biospecimen_ID = Tumor_Sample_Barcode) %>% 
  dplyr::distinct()

# merge sample IDs to filtered ENSG IDs
filtered_ensg <- filtered_ensg %>% 
  dplyr::left_join(consensus_ensg, by=c("Ensembl_ID" = "Gene"))

# merge OpenPedCan cohorts to filtered ENSG IDs
filtered_ensg <- filtered_ensg %>% 
  dplyr::left_join(sample_ids, by= "Kids_First_Biospecimen_ID")

# write to file
readr::write_tsv(filtered_ensg,
  file.path(results_dir, 
            "gene-level-snv-consensus-annotated-mut-freq_dropped_ensg.tsv.gz"))

# Display removed ENSEMBL IDs 
filtered_ensg %>% dplyr::select(Ensembl_ID, cohort) %>% 
  dplyr::distinct() %>%
  tidyr::drop_na() %>%  
  table()

# Display samples in removed ENSEMBL IDs that are in PMTL list
filtered_ensg %>% dplyr::filter(Ensembl_ID %in% pmtl_ids) %>% 
  select(Ensembl_ID, Kids_First_Biospecimen_ID) %>% 
  dplyr::distinct()

# Remove data frames
rm(gene_level_snv, filtered_ensg)
```

#### Variant level SNV frequencies
```{r}
# read mtp table
mtp_file <- 
  file.path(input_dir, "variant-level-snv-consensus-annotated-mut-freq.tsv.gz")
variant_level_snv <- 
  data.table::fread(mtp_file, sep = "\t", showProgress = FALSE) %>%
    tibble::as_tibble() 
# filter mtp table
file_name <- basename(mtp_file)
filter_mtp_table(variant_level_snv, ensg_ids, file_name) 

# Ensembl gene identifiers removed
filtered_ensg <- variant_level_snv %>% 
  dplyr::filter(!targetFromSourceId %in% ensg_ids) %>% 
  dplyr::select(Gene_symbol, targetFromSourceId) %>%
  dplyr::rename(Ensembl_ID = targetFromSourceId) %>% 
  dplyr::distinct()

# merge sample IDs to filtered ENSG IDs
filtered_ensg <- filtered_ensg %>% 
  dplyr::left_join(consensus_ensg, by=c("Ensembl_ID" = "Gene"))

# merge OpenPedCan cohorts to filtered ENSG IDs
filtered_ensg <- filtered_ensg %>% 
  dplyr::left_join(sample_ids, by= "Kids_First_Biospecimen_ID")

# write to file
readr::write_tsv(filtered_ensg,
  file.path(results_dir, 
            "variant-level-snv-consensus-annotated-mut-freq_dropped_ensg.tsv.gz"))

# Display removed ENSEMBL IDs 
filtered_ensg %>% dplyr::select(Ensembl_ID, cohort) %>% 
  dplyr::distinct() %>%
  tidyr::drop_na() %>% 
  table()

# Display samples in removed ENSEMBL IDs that are in PMTL list
filtered_ensg %>% dplyr::filter(Ensembl_ID %in% pmtl_ids) %>% 
  select(Ensembl_ID, Kids_First_Biospecimen_ID) %>% 
  dplyr::distinct()

# Remove data frames
rm(variant_level_snv, filtered_ensg, consensus_ensg)
```

#### Gene level CNV frequencies
```{r}
# read mtp table
mtp_file <- 
  file.path(input_dir, "gene-level-cnv-consensus-annotated-mut-freq.tsv.gz")
gene_level_cnv <- 
  data.table::fread(mtp_file, sep = "\t", showProgress = FALSE) %>%
    tibble::as_tibble() 
# filter mtp table 
file_name <- basename(mtp_file)
filter_mtp_table(gene_level_cnv, ensg_ids, file_name)  

# Ensembl gene identifiers removed
filtered_ensg <- gene_level_cnv %>% 
  dplyr::filter(!targetFromSourceId %in% ensg_ids) %>% 
  dplyr::select(Gene_symbol, targetFromSourceId) %>%
  dplyr::rename(Ensembl_ID = targetFromSourceId) %>% 
  dplyr::distinct()

# read the CNV consensus file
consensus_ensg <- data.table::fread(
  file.path(data_dir, "consensus_wgs_plus_cnvkit_wxs.tsv.gz"), 
  select = c("biospecimen_id", "ensembl"), showProgress = FALSE) %>% 
  tibble::as_tibble() %>% 
  dplyr::filter(!is.na(ensembl)) %>% 
  dplyr::rename(Kids_First_Biospecimen_ID = biospecimen_id) %>% 
  dplyr::distinct()

# merge sample IDs to filtered OT ENSG IDs
filtered_ensg <- filtered_ensg %>% 
  dplyr::left_join(consensus_ensg, by=c("Ensembl_ID" = "ensembl"))

# merge OpenPedCan cohorts to filtered OT ENSG IDs
filtered_ensg <- filtered_ensg %>% 
  dplyr::left_join(sample_ids, by= "Kids_First_Biospecimen_ID")

# write to file
readr::write_tsv(filtered_ensg,
  file.path(results_dir, 
            "gene-level-cnv-consensus-annotated-mut-freq_dropped_ensg.tsv.gz"))

# Display removed ENSEMBL IDs 
filtered_ensg %>% dplyr::select(Ensembl_ID, cohort) %>% 
  dplyr::distinct() %>%
  tidyr::drop_na() %>% 
  table()

# Display samples in removed ENSEMBL IDs that are in PMTL list
filtered_ensg %>% dplyr::filter(Ensembl_ID %in% pmtl_ids) %>% 
  select(Ensembl_ID, Kids_First_Biospecimen_ID) %>% 
  dplyr::distinct()

# Remove data frames
rm(gene_level_cnv, filtered_ensg, consensus_ensg)
```

#### Fusion frequencies
```{r}
# read mtp table
mtp_file <- file.path(input_dir, "putative-oncogene-fusion-freq.tsv.gz")
fusion <- 
  data.table::fread(mtp_file, sep = "\t", showProgress = FALSE) %>%
    tibble::as_tibble() 
# filter mtp table 
file_name <- basename(mtp_file)
filter_mtp_table(fusion, ensg_ids, file_name) 

# Ensembl gene identifiers removed
filtered_ensg <- fusion %>% 
  dplyr::filter(!targetFromSourceId %in% ensg_ids) %>% 
  dplyr::select(FusionName, Gene_symbol, targetFromSourceId) %>%
  dplyr::rename(Ensembl_ID = targetFromSourceId) %>% 
  dplyr::distinct()

# split fusion name into constituent genes  symbols
fusion_names <- data.table::fread(
  file.path(data_dir, "fusion-putative-oncogenic.tsv"), 
  select = c("Sample", "FusionName"), showProgress = FALSE) %>% 
  tibble::as_tibble() %>% 
  tidyr::separate_rows(FusionName, sep = "--", convert = FALSE) %>% 
  tidyr::separate_rows(FusionName, sep = '/', convert = FALSE) %>% 
  dplyr::rename(Kids_First_Biospecimen_ID = Sample, 
                Gene_symbol = FusionName) %>% 
  dplyr::filter(!is.na(Gene_symbol)) %>% 
  dplyr::distinct() 

# merge sample IDs to filtered OT ENSG IDs
filtered_ensg <- filtered_ensg %>% 
  dplyr::left_join(fusion_names, by="Gene_symbol") %>% 
  dplyr::select(-FusionName) %>% 
  dplyr::distinct()

# merge OpenPedCan cohorts to filtered OT ENSG IDs
filtered_ensg <- filtered_ensg %>% 
  dplyr::left_join(sample_ids, by = "Kids_First_Biospecimen_ID")

# write to file
readr::write_tsv(filtered_ensg,
  file.path(results_dir, 
            "putative-oncogene-fusion-freq_dropped_ensg.tsv.gz"))

# Display removed ENSEMBL IDs 
filtered_ensg %>% dplyr::select(Ensembl_ID, cohort) %>% 
  dplyr::distinct() %>%
  tidyr::drop_na() %>% 
  table()

# Display samples in removed ENSEMBL IDs that are in PMTL list
filtered_ensg %>% dplyr::filter(Ensembl_ID %in% pmtl_ids) %>% 
  select(Ensembl_ID, Kids_First_Biospecimen_ID) %>% 
  dplyr::distinct()

# Remove frequencies data frame
rm(fusion, filtered_ensg)
```

#### Fused gene frequencies
```{r}
# read mtp table
mtp_file <- file.path(input_dir, "putative-oncogene-fused-gene-freq.tsv.gz")
fused_gene <- 
  data.table::fread(mtp_file, sep = "\t", showProgress = FALSE) %>%
    tibble::as_tibble() 
# filter mtp table 
file_name <- basename(mtp_file)
filter_mtp_table(fused_gene, ensg_ids, file_name)


# Ensembl gene identifiers removed
filtered_ensg <- fused_gene %>% 
  dplyr::filter(!targetFromSourceId %in% ensg_ids) %>% 
  dplyr::select(Gene_symbol, targetFromSourceId) %>%
  dplyr::rename(Ensembl_ID = targetFromSourceId) %>% 
  dplyr::distinct()

# merge sample IDs to filtered OT ENSG IDs
filtered_ensg <- filtered_ensg %>% 
  dplyr::left_join(fusion_names, by = "Gene_symbol") %>% 
  dplyr::distinct()

# merge sample IDs to filtered OT ENSG IDs
filtered_ensg <- filtered_ensg %>% 
  dplyr::left_join(sample_ids, by = "Kids_First_Biospecimen_ID")

# write to file
readr::write_tsv(filtered_ensg,
  file.path(results_dir, 
            "putative-oncogene-fused-gene-freq_dropped_ensg.tsv.gz"))

# Display removed ENSEMBL IDs 
filtered_ensg %>% dplyr::select(Ensembl_ID, cohort) %>% 
  dplyr::distinct() %>%
  tidyr::drop_na() %>% 
  table()

# Display samples in removed ENSEMBL IDs that are in PMTL list
filtered_ensg %>% dplyr::filter(Ensembl_ID %in% pmtl_ids) %>% 
  select(Ensembl_ID, Kids_First_Biospecimen_ID) %>% 
  dplyr::distinct()

# Remove frequencies data frame
rm(fused_gene, filtered_ensg, fusion_names)
```

#### Gene expression TPM group-wise summary statistics
OpenPedCan collapsed gene expressions TPM matrix only contains gene symbols 
and not ENSEMBL gene identifiers. Therefore, samples associated with removed 
ENSEMBL identifiers cannot be listed. 
```{r}
# read mtp table
mtp_file <- 
  file.path(input_dir, "long_n_tpm_mean_sd_quantile_group_wise_zscore.tsv.gz")
tpm_group_wise_stats <- 
  data.table::fread(mtp_file, sep = "\t", showProgress = FALSE) %>%
    tibble::as_tibble() 
# filter mtp table 
file_name <- basename(mtp_file)
filter_mtp_table(tpm_group_wise_stats, ensg_ids, file_name)

# Ensembl gene identifiers removed
filtered_ensg <- tpm_group_wise_stats %>% 
  dplyr::filter(!Gene_Ensembl_ID %in% ensg_ids) %>% 
  dplyr::select(Gene_symbol, Gene_Ensembl_ID, cohort) %>%
  dplyr::rename(Ensembl_ID = Gene_Ensembl_ID) %>% 
  dplyr::distinct()

# write to file
readr::write_tsv(filtered_ensg,
  file.path(results_dir, 
            "long_n_tpm_mean_sd_quantile_group_wise_zscore_dropped_ensg.tsv.gz"))

# Display removed ENSEMBL IDs 
filtered_ensg %>% dplyr::select(Ensembl_ID, cohort) %>% 
  dplyr::filter(cohort != "All Cohorts") %>% 
  dplyr::distinct() %>%
  tidyr::drop_na() %>%  
  table()

# Remove summary statistics data frame
rm(tpm_group_wise_stats, filtered_ensg)
```

#### Gene expression TPM gene-wise summary statistics
OpenPedCan collapsed gene expressions TPM matrix only contains gene symbols 
and not ENSEMBL gene identifiers. Therefore, samples associated with removed 
ENSEMBL identifiers cannot be listed. 
```{r}
# read mtp table
mtp_file <- 
  file.path(input_dir, "long_n_tpm_mean_sd_quantile_gene_wise_zscore.tsv.gz")
tpm_gene_wise_stats <- 
  data.table::fread(mtp_file, sep = "\t", showProgress = FALSE) %>%
    tibble::as_tibble() 
# filter mtp table 
file_name <- basename(mtp_file)
filter_mtp_table(tpm_gene_wise_stats, ensg_ids, file_name)

# Ensembl gene identifiers removed
filtered_ensg <- tpm_gene_wise_stats %>% 
  dplyr::filter(!Gene_Ensembl_ID %in% ensg_ids) %>% 
  dplyr::select(Gene_symbol, Gene_Ensembl_ID, cohort) %>%
  dplyr::rename(Ensembl_ID = Gene_Ensembl_ID) %>% 
  dplyr::distinct()

# write to file
readr::write_tsv(filtered_ensg,
  file.path(results_dir, 
            "long_n_tpm_mean_sd_quantile_gene_wise_zscore_dropped_ensg.tsv.gz"))

# Display removed ENSEMBL IDs 
filtered_ensg %>% dplyr::select(Ensembl_ID, cohort) %>% 
  dplyr::filter(cohort != "All Cohorts") %>% 
  dplyr::distinct() %>%
  tidyr::drop_na() %>%  
  table()

# Remove summary statistics data frame
rm(tpm_gene_wise_stats, filtered_ensg)
```

#### Methylation gene-level summary 
OpenPedCan contains methylation and rnaseq summaries of cohort cancer groups and
can't not associate with samples. Therefore, samples associated with removed ENSEMBL 
identifiers cannot be listed. 
```{r}
# read mtp table
mtp_file <- file.path(input_dir, "gene-methyl-beta-values-summary.tsv.gz")
gene_level_methyl <- 
  data.table::fread(mtp_file, sep = "\t", showProgress = FALSE) %>%
    tibble::as_tibble() 
# filter mtp table 
file_name <- basename(mtp_file)
filter_mtp_table(gene_level_methyl, ensg_ids, file_name)

# Ensembl gene identifiers removed
filtered_ensg <- gene_level_methyl %>% 
  dplyr::filter(!targetFromSourceId %in% ensg_ids) %>% 
  dplyr::select(Gene_symbol, targetFromSourceId, Dataset) %>%
  dplyr::rename(Ensembl_ID = targetFromSourceId, cohort = Dataset) %>% 
  dplyr::distinct()

# write to file
readr::write_tsv(filtered_ensg,
  file.path(results_dir, 
            "gene-methyl-beta-values-summary_dropped_ensg.tsv.gz"))

# Display removed ENSEMBL IDs 
filtered_ensg %>% dplyr::select(Ensembl_ID, cohort) %>% 
  dplyr::distinct() %>%
  tidyr::drop_na() %>% 
  table()

# Remove frequencies data frame
rm(gene_level_methyl, filtered_ensg)
```

#### Methylation gene-level summary 
OpenPedCan contains methylation and rnaseq summaries of cohort cancer groups and
can't not associate with samples. Therefore, samples associated with removed ENSEMBL 
identifiers cannot be listed. 
```{r}
# read mtp table
mtp_file <- file.path(input_dir, "isoform-methyl-beta-values-summary.tsv.gz")
isoform_level_methyl <- 
  data.table::fread(mtp_file, sep = "\t", showProgress = FALSE) %>%
    tibble::as_tibble() 
# filter mtp table 
file_name <- basename(mtp_file)
filter_mtp_table(isoform_level_methyl, ensg_ids, file_name)

# Ensembl gene identifiers removed
filtered_ensg <- isoform_level_methyl %>% 
  dplyr::filter(!targetFromSourceId %in% ensg_ids) %>% 
  dplyr::select(Gene_symbol, targetFromSourceId, Dataset) %>%
  dplyr::rename(Ensembl_ID = targetFromSourceId, cohort = Dataset) %>% 
  dplyr::distinct()

# write to file
readr::write_tsv(filtered_ensg,
  file.path(results_dir, 
            "isoform-methyl-beta-values-summary_dropped_ensg.tsv.gz"))

# Display removed ENSEMBL IDs 
filtered_ensg %>% dplyr::select(Ensembl_ID, cohort) %>% 
  dplyr::distinct() %>%
  tidyr::drop_na() %>% 
  table()

# Remove frequencies data frame
rm(isoform_level_methyl, filtered_ensg)
```

## Session Info
```{r}
sessionInfo()
```